As far as i know optics of the Assimilated set apply not unly to Federation and Klingon ships, but to ships belonging to different factions as well (you can see it by using a Ferengi holo emitter while having the Assimilated set equipped).
In my opinion NPC Borg ships encountered in game could consist not only of native Borg ships but also from assimilated ships belonging to other species. This would increase the variety of Borg (and the diversity of Borg related encounters) with probably not much effort, since ship models with corresponding optical modifications already exist.
I like the idea. Would be interesting to fight against an assimilated Keldon which calls in its Photonic Fleet or an assimilated Breen Crusier with SNB, or... well there are many good encounters possible. But in the end it has to fit in the story.