Protection against automotive power supply hazards
Load-dump
... is a killer - your TVS has to turn a huge amount of energy into heat without going pop.
ISO7637 for a 12V system has a spike peaking at up to ~90V with a rise time of 5-10ms lasting up to 400ms from a source resistance as low as 0.5ohms. That's several hundred Joules of energy in less than half a second!
Not all of that has to go into the suppressor - only the excess above the clamping voltage (but still ~60V in your case)
On the bright side, load-dumps are pretty rare, so if it's a one-off and you don't mind the small risk, you could ignore it.
Fast transient spikes
These can reach 200V when the wipers switch off for example - provide a (high-voltage-rated) capacitive route for those to ground right near the input.
Longish-term over-voltage
Automotive electronics is often specified to survive 24V for several minutes (for when a car is jump-started off a 24V truck) and 48V for up to a minute (IIRC) as sometimes 2 truck batteries are used to provide a quick boost charge to get a car moving in extremis! Your spike suppressor may pop under those conditions.
Dropouts
Battery dropouts can also be significant, there's a test in the industry which involves a series of pulses battery voltage falling to 0V - you need to have enough internal capacitance to keep your supply rails up when that happens.
Real-world requirements specification
If you want an example of how gory this can get, Ford's electromagnetic compatibility (EMC), which includes transient testing, is available on the web:
Component EMC Specifications EMC-CS-2009
Search through it for "transient" and "dropout" to see what series-production designs are supposed to live up to!
You seem to have answered your own question. The LTC4365 is probably a good solution. The datasheet says no TVS is needed, but I still would use one.
Have the LTC4365 followed by a buffer capacitor to handle dips in the battery voltage. If the battery is also used for a starter motor it's probably unavoidable that the voltage drops, especially when you're consuming 15W (that's 4.5A at 3.3V).
If the capacitor has a rather large value you may want to use a slower fuse, otherwise it may blow when switching on. (The fuse doesn't offer extra protection over the LTC4365 other than limiting the damage in case of a component failure).
Any particular reason why you want to use an isolated DC-DC converter? They're usually not needed for battery operation.
If you've already got a isolating DC-DC converter that can handle up to 36V in, it doesn't sound like you need much more. I don't understand what you think the LTC4365 will do for you. Your converter can already handle 36V on its own, which is actually a little more than the 34V the LTC4365 is rated for.