How does Ubuntu flavor iso differ from a desktop package?
It's quite common for users to want to "try" other flavors by installing say flavor-desktop rather than by trying out a whole new iso, either in a VM or in another partition, which, in my opinion, is the cleanest option.
As you've noticed, the grub screen, the login and logout screens could all be altered without warning.
Menus may contain duplicates. Two text editors, two screenshot tools, etc.
Some default applications may lose their default status.
Notifications may appear different. A classic case is when one adds the xubuntu (or lubuntu) desktop to Unity! That's because the notification system of xu/lubuntu takes over and the effect persists even after logging out and back into a Unity session.
Reversing the installation of flavor-desktop isn't trivial. The standard discovery is that deleting flavor-desktop doesn't do anything other than remove the metapackage. All the packages installed by the metapackage remain.
Re. Canonical, it provides Ubuntu. The other flavors are community-driven with Canonical providing infrastructure and hosting and more: check out Jeremy Bicha's post. Other than ensuring that flavors meet certain minimal requirements, Canonical is quite "hands off".
I think it isn't stressed strongly enough that one can mix certain desktop environments provided an adequate amount of research homework is done beforehand!
In short, depending on the type of assitance you intend to provide, a clean iso install would be the best option.
Here are just a few Ask Ubuntu links on the topic:
Restore Unity after uninstalling Mate
How to change splash screen Ubuntu back?
What are the risks if install a secondary desktop environment / interface on my ubuntu?
Installations from ISO image and metapackage are no different, when metapackages are installed from server ISO and minimal CD images. Users who use an official ISO image and purge packages of existing flavour, then install packages of another flavour may see no difference as well.
Therefore, the metapackages could provide same installation as the ISO images. The following sources seem to support the similarity.
Lubuntu community has suggested its metapackage in this page on Lubuntu Wiki.
[...] use the server ISO. When prompted as to what to install unmark everything (space bar) except basic server and press tab to get to OK. Once installed, login and then do:
sudo apt install lubuntu-desktopto add in the lubuntu system [...]
Ubuntu community has mentioned its metapackage in this page on generic Wiki, albeit bit outdated to this answered date (since Ubuntu now installs Unity instead of GNOME).
[...] For example, the ubuntu-desktop metapackage installs the full GNOME desktop environment, with all the other packages that are in a default Ubuntu install. The existence of meta-packages makes it very easy to install other Ubuntu derivatives on your desktop; [...]
This other page on generic Wiki has mentioned similarly.
[...] For example, an Ubuntu user can install the Kubuntu environment (KDE and all its associated programs) by selecting "kubuntu-desktop."
The last mentioned page also has listed metapackages by category, and the relevant ones are the first two: "Desktop Metapackages" and "Ubuntu System Metapackages". This simply means "KDE" does not equal to "Kubuntu", "Xfce" does not equal to "Xubuntu" and so forth.
Revised answers
what differentiates the pre-made Ubuntu flavor iso from installing a package ?
No difference for the installation itself. What differentiates between the two is the user experience of installing the product. This is a big deal for end users who expect the product to be available in appropriately packaged form, rather than installing the relevant metapackage via Terminal.
Is it all the same base underneath the hood or does installation from iso have specific configurations ?
Yes, both installations have same settings. This is achieved by installing the "default settings" package for respective flavours, except Ubuntu one is named as ubuntu-settings. Usually, the "default settings" package is already a dependency of respective metapackages.
However, ISO image itself is different because it must contain the installer and additional packages to be bootable and installable. The resulting installation is the same because these packages will be removed later; The installer itself will not be available on local machine once installed.
If it's possible to install a flavor via package manager, why then separate flavor iso's exist ?
A product is most meaningful when tangible and works as advertised. ISO images are more tangible than the metapackages. ISO images will work as advertised upon made as bootable discs. The metapackage will require some knowledge and effort to make it work and not quite a product.
Revised evaluation
It is important to note that metapackages in this answer mainly refers to metapackages for Ubuntu and its flavours. These shall not be mistaken for metapackages of particular desktop environment such as GNOME, MATE, Cinnamon and RazorQt. While Ubuntu and its flavours can have multiple metapackages, user will just have to look for *-desktop metapackages for relevant ones.
Finally, returning to the top question:
TL;DR: how does an Ubuntu flavor iso installation ( for example Lubuntu ) differ from installing a desktop package via apt-get ? (for instance sudo apt-get install lubuntu-desktop)
I have named three differences: User experience, more tangible, works as advertised (or as intended). For end users, less knowledge and less effort are required for installing from an ISO image when compared to installing the metapackage.
User convenience is another thing, but not necessarily applicable to all ISO images. For example, a minimal CD is convenient for small size to download but has more steps for installation. The minimal CD is useful to prepare custom installations, thus offers flexibility rather than convenience.
When users gain more knowledge and more experience, they are less likely to notice the differences. Both experienced and power users can now use Ubuntu and its flavours easier, but the challenges faced by beginning users have not changed.
Like any beginning users, I was once an ignorant user who couldn't even make a bootable disc from ISO image. I'd have not noticed these differences until recently, I remembered that I was once a beginning user. Above all, I'd always prefer the official ISO image for clean installation.
Disclaimer
This answer is the revised approach based on my experience as beginning user, which is more relevant for end users. The following applies.
I did not actually compare installation from ISO image and installation from metapackage, side by side. There are supporting facts that could tell these are technically the same.
I could not find relevant views of Canonical or leading members of community; This answer only contains my own views, findings and facts from the Web.
TL;DR Installation from ISO image is technically the same as installation from metapackage, provided the base system has no other flavour and the correct metapackage is installed. ISO image is more tangible, will work as advertised and close to the actual product.
Related posts on Ask Ubuntu
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Should I use tasksel, tasks in APT or install regular metapackages?
How remove all programs from a meta-package?