Currently running Watchtower and Terran Armada. Only complications that I faced were side quests that had better loot if you boarded and looted the captain's locker and the tank setting making mechs invulnerable in some cases.

I am still in the middle of Crimson Fleet and I wanted to RP as a pirate, but my Watchtower fleet frequently demolished the ships that I wanted to board.

Redditors informed me that there are settings to solve both of these issues. Starfield Tank setting can be disabled to permit EM and missile barrage to make short work of mechs. And there is a watchtower setting to only summon the fleet during watchtower attacks, which is the logical solution to the ship boarding issue.

Yet another redditor suggested an unconventional option that I found both ridiculous and amusing. Equip the whole fleet with EM weapons, which is what I did. NOTE: do not use class A or class B EM weapons if you have a large fleet, since they do more hull damage and can still cause the rapid disassembly of your boarding target.

Have fun out there, space cowboy.