How to tell apt that dependencies are resolved manually?
You should use the equivs package to generate meta-packages that provide these dependencies, and then use dpkg to install these packages.
Installing equivs and reading its documentation should be enough, but this guide for Ubuntu is quite extensive and should apply to other APT systems as well.
Also, if you feel that a package should be able to be installed without the specified dependency, you should file a bug against the package, explaining the case where the dependency is not needed.
In this case, texlive-base-bin seems to only be "Recommended" and not a "Dependency" in the base Debian distribution at least (probably in part since texlive is such an enormous package), but because it is common to install upstream TeX Live on Debian since the distribution version often lags behind greatly (for the reason that the package is such a beast that it often can't be packaged without substantial work, which is mostly done by one or a few persons, who claim they have lives beside Debian), the equivs trick is often used with TeX Live (wow, that sentence got out of hand :-) ).
Addition: For more detailed instructions for those looking to install TeXLive outside of the package system, these instructions on TeX.SX are more extensive and will most likely continue to be kept updated. They also include more explicit instructions regarding the equivs step.