1) I have to run the game with forced dx11 to make all load times faster, particularly post battle load times. With DX11 they are 10-20 seconds, without they are 3-4 mins. My pc is top of the line (at least for Rome 2) so it has nothing to do with specs, running the game this way is non-negotiable for me to actually enjoy it.

2) However, running on dx11 stops all mods from loading into the game. So essentially, I have to choose between a modded but slow experience or completely vanilla and optimal experience.

3) Can anyone help me find out why this is happening?

To test it yourself to see what I am saying you can set your game to dx11 by going to steam library-properties-general tab- and in the launch options below type -dx11 exactly like that. Close the window, and run the game. Do not hit continue campaign, for some reason it won't run dx11 that way and all mods will be enabled. Hit play and dx11 will be enabled, all performance will be increased, BUT no mods.