GZ (pre-pbr/divisional league) had a Random Terms Generator w/ Variants (the TRBGV). It would give you all the stuff the RBG would give PLUS tell you what variants to take.
You are right though - you do run into situations where forcing variant selections can benefit one race over another.
You could take a novel twist on this though: For certain games, make it a 'line' match. Basically, you can use the PBR matrix to say ALL listed ships are restricted. You'd then be left with nothing but line ships. Or, you could use variantions on this theme: Command Only or Support only or Carrier groups only (a little problematic here with the PF races - but you get the idea)
The bottom line is, you can use the existing PBR frame work and apply it in different ways to create games that have a very differnt flavor.
Why the 'line' match? PBR came out of my desire to ultimately see more vanilla ship matches. I can remember lining up 3xCA v 3xD7 matches with the boys in old 3rd fleet and they were a blast. That or the D6 v Mirak CS matches I would sometimes play with Kraven. In the end, I settled on taking set SFB rules (S8) and converting them. This largely eliminated rampant cheese and created an environment where new ship line ups became prevalent.
However, over time, I found that - from my perspective - the old cheese fests were replaced by new versions of those cheese fests: almost every PBR match seemed to consist of 1 Command, 1 support (usually the cheese ship) and the one token line ship they were forced to take. It's still better than the old way (IMO), but still didn't hit the mark on what I wanted.
In my highly romanticized view of things, game that were match ups of pure line ships was simply the ideal: D7/6's, D5's, F5's, E4's v CA's, CL's, NCL's, DD's, FF's - that kind of thing. Refitt them (B or K's for Klinks, +'s for the Feddies) but leave of the droners, fast ships, carriers, escorts, maulers, ect. Go ahead and throw in one command ship for flavor if you like.
Anyway, something you can think about. I don't think applying a 'Line Only' or 'Command + Line' only (all other PBR rules apply) to some games in a match would necessarily create any inherent imbalance....but then I hardly play anymore so what do I know