Mods that have modified versions of the same file will automatically report as incompatible even if the file is the same.

The workaround to his is to set one mod as an override to the other.

OK. Thank you. WOW, I get dolynick himself to answer my question. I am a complete noob when it comes to mods. How does the override work? I want the Alternative Interface Mod to work, but I also want the SR Community Patch Mod to work. If I set the CP mod to Override the Alternative Interface mod (AImod), does that mean the AIMod will not do anything? Or do I set the AImod to override the CP mod?
Also, I see the button that says "Override" in the in-game mod manager, do I just push that button while the mod I want to take precedence it open?

Overrides are done in the modinfo.txt using the "Derives From:" command.

The mod that derives from: is the one that loads last in the order and will overwrite similar files in the derived from mod. In your case you would want your Althernative Interface to derive from the CP patch and override any conflicting filenames.

Of course, if you do this, you have to make absolutely sure you're not overwriting anything different and important from the CP files. If you do, you may well end up with crashing.

Another interesting effect of the Derives From command is that you don't actually have to enabled the referenced mod anymore. You could just enabled your AI mod alone. I generally recommend you enable it anyways but technically it's not actually required.