You were right, and it wasn't just most combinations, it was every projectile round in the game. They were being fired from the world's centre point, which happens to sit inside the train by the doors, instead of from your gun. That's why it looked like your shots came out of a door. Restarting seemed to fix it because it depends on where you're standing.
Fixed now, along with two other aiming problems: shots landed slightly beside the crosshair while you were turning, and monster hitboxes were smaller than the monsters, so hits on arms and wings could pass straight through.
Thanks for reporting it. That one comment led to finding the worst bug in the game.
Thanks for playing it through and for the detailed write-up, this was the most useful feedback I got.
You found a real bug. Every projectile round (BOOMSTICK, BOLT, SEEKER, SAW, PINEAPPLE) was being fired from the middle of the train instead of from your gun, so they hit walls or went nowhere. Hitscan ammo like ARC was unaffected, which is why swapping to boomstick broke your run. Fixed, and there's now a test that fires all 14 ammo types at targets and checks each one does what its card says.
Your main point was the better one though: once you have a good gun, almost everything you're offered is a downgrade. So the shop now grows with the run and stops offering junk commons later on, and every fifth station belongs to JEFF, a dealer with a stall on the platform who sells 30 epic and legendary mods for scrap. No monsters at his station, so you can shop in peace.
Also, since you liked the gun: no bullet spreads any more, every pellet goes exactly where you aim, and nothing ricochets.
More combat variety is next on the list, along with new station layouts.
