CaliberX itself adds things to all the leveled lists for Ammo, they were always tiered in both games.
If ammo doesn't spawn with, or incorrect ammo with the WEAPONS then the WithAmmo (the list all have WithAmmo in the name) lists for those WEAPONS are incorrect.
Fallout 3 doesn't and did not ever use some of the lists that NV does, so they are limited. The only reason anything from NV spawns on those vendors is because TTW added those items to those lists. Adding things to their chests is not the correct way to add things, you should add them to the lists instead.
Someone needs to make a WotNM patch for TTW and CaliberX specifically to have full integration. That person is not me, however I expect that darthbdaman will probably make such a patch if he hasn't already.