I haven't tried your script yet, the comments came from looking at the code itself. I've got this weird thing about my start button, I just really don't want to mod it and I can't explain why, which is why I haven't installed your mod…although I suppose I'll have to to test the parser once I finish it.
When I say command-line, I mean out-of-game. I'll be writing the parser in C++ (mostly because it's what I'm most comfortable with) so that it can be run from within the EQ2 game directory. As far as I know of there's no way to even parse the information in-game, let alone save it to a custom file, and I'm pretty sure any way to do it would in some way be a violation of the EULA. Besides, the XMLs are only polled on load, so altering the custom profile XML in-game wouldn't really do any good, you'd have to restart the game to get the changes to take.
As for splitting the custom button out to its own XML, basically you just cut that portion of the code out of the startbutton XML and replace it with
Code:
<Include>eq2ui_mainhud_custompreset.xml</Include>
then paste the cut code into eq2ui_mainhud_custompreset.xml or whatever you want to call it.