I'll necro the thread and answer, in case someone is wondering, as I tried playing with both at the same time.

Currently, it seems to work fine, except for the last tier of Starbases in that mod, which gets bugged and will not fill weapon slots it receives from modules, instead leaving them empty. Which is, surprisingly not that big of a deal, considering how ridiculously beefy it is and that it still ends up with more firepower than citadels by virtue of its default weapons alone (aswell as twice the FP).

It kind of sucks not to be able to customize its weapons though.

i think ive had the same issue

@VXHunter; could this be fixed somehow?