It seems like XPression always tracks what the highest scene # used was, regardless of which scene numbers are currently in-use. So if you created two scenes, #1 and #1000, the next scene you create will be #1001. I'm with you on wanting to be able to "reset" this counter and use the currently active scenes, but only from an OCD standpoint as yours.
I've also found that if you're in a multi-box setup (for example, running XPression along with iNews and MOS Gateway as we are here), XPression only cares about the scene number when creating scenes in the sequencer. So if I were to have two XPression machines that weren't "in-sync" when it comes to scene numbers, scene #1 will be different depending on which machine I set it online.
#XPression