This wasn't the answer, since using 10+ with any ROM that is not encrypted doesn't result in Extracted files to begin with. I did, anyways, update to V9 to no different results.
I have kept doing more trial-and-error solving in the meantime though, I'll make them as clear as possible, so sorry if I sound redundant at times:
I came to notice one thing in an altered ROM of Omega Ruby: Trainers with the "Moves" box in the "Trainer Info" tab of the Trainer Editor have their moves DELETED BY DEFAULT. To fix this I'd have to check the individual boxes of hundreds of random trainers and manually add their moves back.
Addition to this point: I've recently seen a video where a guy explains how to use this tool. The video is quite old, so he is probably using an OLDER VERSION OF Pk3DS, and I DO NOT KNOW HOW RELIABLE THIS SPECIFIC PIECE OF CLUE IS, but in it, when he clicks randomize (see: Skip to 34:41 if it doesn't do it automatically) when the program is running through every trainer you can clearly see that MOST of them have the "Moves" box unchecked. I wonder if that also means that they don't have moves, just like in mine.
I have recorded a gif of the problem for easier pinpointing. Maybe it is obvious that "yeah, the Moves box is there to specifically delete all moves in a Trainer" but since I doubt the usefulness of that, I'm thinking there's a problem. What I THOUGHT it did was select exactly which Trainers you'd want to mess with their moves, so an unchecked box meant they were locked but it should display the move names in the grey boxes. Instead they are empty and the Trainers thus only do Struggle over and over with all their pokemons.. And if IT IS working as intended, I'm still questioning the fact that AS SOON AS I USE PK3DS ON MY EXTRACTED FOLDERS IT DELETES MOVES OF 70%+ OF THE TRAINERS: (This was recorded on a freshly and pre-tested Rising Ruby ROM)
On another note: The problem could be from three things: the ROM itself, pk3DS or the Toolkit. The ROM itself has no problem as this was the first thing I tested, booting up both the Rising Ruby and vanilla Omega Ruby without any changes to them. Both worked fine.
I then tested the extractor! I picked a ROM, extracted their folders and then remounted them. I also got in contact with the creator of the extractor over at twitter and they said it wasn't something their tool could do. And it is true, after the proccess, the remounted ROM also showed no problems whatsoever.
In conclusion, this really seems like a problem in pk3DS. Since I don't intend to do any major changes to Trainers in my run (only meant to add random prizes at a low-ish %) I'm going to try and use the randomizer on a working ROM WITHOUT EVER OPENING THE TRAINER TAB, since this program seems to apply changes and save them AUTOMATICALLY, which really looks like an oversight at times. And see if that works. I'll be only randomizing pokemon abilities and starters.
In the meantime, if someone can also help look into this or shed some light on the problem like "oh this tool specifically doesn't work on Ruby because of this issue, sorry", that would be great. Thanks in advance.
Reporting error I got while trying to change Stunky's moveset during my proccess, specifically I lowered all his moves by 3 then tried adding Sucker Punch at level 34, I then click on the "Level" tab, just to organize it in order, which got me: