Oh, I think I can see the behaviour you're speaking of - but I don't think it's quite the same issue. Eg:
Condor
- equipped with 1x Claw, 1x empty bay, will stay on REGROUP (unless an opportunity arises)
- equipped with 2x Claw will ENGAGE by default
Heron
- equipped with 1x Claw, 2x empty bay, will stay on REGROUP (unless an opportunity arises)
- equipped with 2x Claw, 1x empty bay will ENGAGE by default
Astral
- equipped with 1x Claw, 5x empty bay, will stay on REGROUP (unless an opportunity arises)
- equipped with 2x Claw, 4x empty bay will also stay on REGROUP (unless an opportunity arises)
- equipped with 3x Claw, 3x empty bay will ENGAGE by default
That sounds about right for what you're referring to, right? It's slightly different for these modular carriers where they actually will be set to ENGAGE but have essentially the same behaviour because they don't have a CARRIER_FIGHTER_TARGET selected.
Checking a little more, the modular carrier issue even occurs with some lopsided fits with non-zero numbers of bombers. The Roider Union Ranch-class has 4 bays,: 2 built-in Breaker Drone wings (3 drone fighters with 4000 engagement range at 2 OP if they weren't built-in) and 2 modular ones. After equipping an additional Breaker Drone Wing and a Trident in the modular slots it will stay passive (but it engages properly if both modular slots are set to bombers).
Soo given it happens even when fitting bombers it's possibly an unrelated issue? Anyhow, thanks for checking into this!