In each vanilla generator appears this text as part of a comment:

(If you want to replace the generator entirely, in case you have an extremely specific item pool in mind, you should
get rid of declaring scriptstorun and the "for scriptname in scriptstorun" bit. - but note it will no longer be quite as
compatible with other mods.)

This is a leftover from Wibi (hi!)'s clumsy implementation of flexible generators (originally just for Warrior 1, extended by Jackeea to all episodes), where everything was self-contained in the generators rather than there being a separate flexible_generator.hx script. Jackeea forgot to change this comment, basically.

What it means with the current functionality in mind is that if you want a generator with just your items that doesn't let other mods add anything, you should get rid of declaring itempools and remove the runscript that fills itempools, and instead just write out the contents of each list used in the generator by hand.