Well, it depends on how you're doing the tweaking.
There are 2 major ways you can do it and I'm just paraphrasing @Kyler2 here lol.
#1: You copy paste the .gd file (the script) that you want to modify and then modify it, making it replace the WHOLE shebang. This is done when you have no other choice, like, say Scripting a new "Special" type of encounter such as the Treasure chest, or the slavers you meet near Gorn. In other words, you should only use this if there is NO other way around it using...
#2: You make use of the <AddTo X> tag provided by @Strive4Power and add the code you need for that script without having to rewrite and replace the whole thing, which is much more Multi-Mod friendly. Only setback is, in order to use this one the information you want to add/modify MUST BE INSIDE one of the following: 'var', 'onready var', 'signal', 'function' or 'class'.
One of the advantages of this project is, both the regions, and the enemy data (encounter groups, enemy stat blocks, captured people parameters and enemy equipment) are stored in a 'var'. The whole Database is. Making addition through <AddTo X> tag seamless AND harmless at the same time, you just put:
<AddTo 0> var enemygrouppools =
And you start adding stuff. Now, I checked the item database, and at least the item list--which is where all the item names, stats and effects are listed--is inside a single 'var' so adding new items wouldn't be a problem... IF they don't have any special/non-existing effect in the code, because if they have you would need to then define those in NEW functions inside items.gd and that means you are no longer in need of #2, but rather #1... So you might as well do all the changes directly onto the code, because otherwise you would need 2 mods for tweaking it (You can only have 1 .gd file of each name in a single mod folder, so you can't do both #1 and #2 at the same time without creating 2 mods... yeah.)
@Strive4Power PLEASE, make a tag that just ADDS to the end of a script whatever you write below it. It would make modding and mod compatibility so much easier...
@AricTriton If you want to join forces I'd be more than glad to do so, I intended this to be a community mod anyways, lol.
EDIT: SCRATCH ALL THAT, tried it, since I started working on this thing this morning and I've been figuring shit out along the way, tried to make the transition, got NOPED so hard by the game, it wasn't even funny... So yeah looks like figuring out how the hell is the <AddTo X> function adding stuff to a "var = {" line of code is going to be fun I guess... Back to the drawing board.