The reason people fix bad gouges in their bases with Ptex is because it affects the ride and affects the core. Would something on the bottom of the board affect the ride since that's the part touching the snow? Would a bump on the bottom of your foot affect walking? The answer is YES. It may not be a really noticable difference, so just ride it, but obviously anything not level on the base will affect riding to some degree.
The screws fit into the board, not the bindings, the inserts are the specific thread, so yes you should've used the correct screws. At least you didn't strip out the threads in the inserts, so look on the bright side, you can still ride it. If it really is exactly same length and same thread, you may have just tightened them down too much. Back them off, leave it, and tighten it down to a reasonable level before you ride next time.
Off topic a little: I recently talked to the dumbest snowboard instructor in the world last week regarding something similar. He's riding an X8 and as I was walking to the lodge he stopped me and asked if my base came with bumps in it. I told him no, my base is flat. He said "Feel this...". Where his screws were there were nipples. He then blamed it on the channel and said it must be that coming through his board. He also used a drill to tighten them down. I just shook my head and walked away.