If the transmission is ever so slightly too deep, you can compensate by not screwing the refill in all the way. Slimline transmissions work just fine like that. I've backed out refills a turn in the past when their lengths have varied.
I've found that both transmissions and refills vary from vendor to vendor, and kit to kit (sometimes even within the same batch). I use a slightly long press-block to get close, and make the last adjustment to fit.
On those occasions when I slip and go too far, I disassemble and start over. If I'm trying to salvage the transmission, I'll pull the bullet (with an inertial puller) and drive the transmission out with a punch. Then I'll soak the case and bullet in acetone to remove the powder coat. All the pieces can be repolished and reassembled later.
If I don't care about the transmission, I'll just drop the entire thing in acetone. Since I use CA glue on the tube, it comes out along with the transmission. The acetone will also dissolve the lube in the transmission, so I don't reuse it. At that point, however, I can repolish and recoat the cartridge without having to reseat the bullet.
I hope that helps,
Eric