I had a similar issue with Vayras Sector prompting me to delete it (though I plan to play around with it next playthrough) - the added d-mods combined with the vanilla ones caused some ridiculous scenarios. Namely, recovering an atlas freighter that had 0 cargo capacity. Then, after a while, I got a prometheus with 0 crew capacity whilst requiring skeleton crew and I think it had 0 fuel capacity as well, which just *** me off enough to delete the mod.
As for SWP, if you also have Nexerelin, it can sometimes be cheaper to not recover the IBB ship, but to buy it from Prism Freeport later on. You can also tweak the settings to make Prism Freeport sell IBB ships regardless of IBB mission progression, as well as a tweak that lets you keep buying the same ships even if you bought one or recovered one.
All in all, sure, some of these IBB ships are nice, but, considering that you generally fight a full-on overpowered fleet with the IBB ships ALWAYS having loadouts that require more OP than they actually have, the whole IBB thing seems like just an endgame activity to me. By the time I can safel get those ships, I probably no longer need them, if I have a fleet that can handle its bounty, and it being weaker than what I have to fight is also a bit of a letdown.
Though, as I get, they are strong in terms of being strong for their DP value, so I guess there's that, but still.
I'm sure you're already aware of this, but the new d-mods Vayra's Sector now adds to the game make auto-recovered IBBs really, really bad. You might want to consider reducing how many d-mods an auto-recovered IBB ship gets slapped on it.