All fixed in the latest version.

There is no such thing as an 'undeserved' win. Never mind that these classes are added to NPCs as well, which tends to balance things out quite a bit. Your suggestion of splitting them up to prevent 'cheating' actually makes things easier, because then you have the fairly easy to kill vanilla rogues instead of the pure murder of toxin dispensers at times.

As for the mod itself:

Personally, I like the added utility in the secondary trees. What has always irked me a bit about Bulwark was that it has access to things like archery or twohanded weapons and no real incentive to use them, because shield combat is just so much better. I'm not sure how to fix this entirely without making, say, skirmisher superfluous, but it's been a nagging thought in my head ever since I saw 'bulwark rework'. Maybe mirroring IRL and allowing a buckler to be equipped with a twohanded weapon would work? That seems like it may be a bit OP, though, and doesn't really address that the lack of synergy with the talent trees in question is the real elephant in the room.

Out of curiosity, why does it make you sad? Should we take away "undeserved" wins from people who scored easy victories when Solipsist and Oozemancer were brokenly overpowered at release? Is it "undeserved" if somebody won by abusing Saw Wheels Sawbutcher or the totally broken release Pain Enhancement System? How about people who win insane using item vault nonsense? Are those undeserved?

I dunno, I feel like this isn't a big issue since anyone who wins with the Bastion mod is going to have the mod on the cvault winner sheet.

Ideally I'll eventually have one big class rework mod, where you can toggle what you want to have. I'd split the generic changes of stuff like Survival/Mobility into a seperate thing, for people that don't want new classes but just like general stuff.