I'm not sure I see the connection between this and game maker

I stopped using Game Maker when YoYo Games became corporate sellouts and stopped offering a "Unlimited Lite" version.

What do you mean, that this is a problem unique to Game Maker? I'm not sure how this wouldn't be fixable within the limits of GM. It's generally possible to do just about anything, and this doesn't seem like it would be hard to fix.

The problem is, for every workaround you make to avoid Game Maker's shoddy collision system, you end up with junk data and processes because those things built into GM are impossible to delete/deactivate.

Doesn't the YYC deactivate them? It's way too expensive for now necessary it really should be, though...

Personally I don't use any of GM's built-in stuff. I make my own movement and collision detection systems, because I really prefer to have full control over where and how those pieces of code are executed.
Though you don't necessarily need to use a workaround to their collision system. It looks like the pickup items were able to intersect each other somehow, so maybe there's somewhere in the code for putting down picked up items where you can force move them out of collision or not allow players to put stuff down in a place where it's intersecting.

Personally, though, I just think GM is too limited in a lot of ways to be worth spending so much time with it anymore. It doesn't do HD games very well, it's absolutely awful at allowing multiple resolutions unless it's totally fine to have your view vastly expanded for players depending on their screen size (or you're fine with foregoing fullscreen completely), and there's really no way to zoom in or out at all. I've played enough commercial games made in GM to know that it doesn't handle lots of stuff going on at once the way other engines seem to be able to. Risk of Rain is an awesome game, but something running at such a tiny resolution with such small sprites should NOT lag nearly as much as that game does, and I'm pretty sure that has a lot more to do with GM itself than the developers making unoptimized code.

Pixel-based collision checking and storing every numeric value as a double adds to it. The problem with writing your own code is that the existing GM mechanics still exist, is what I meant to say. You can't redefine or delete them, just work alongside them as they leech valuable cycles from your processor. It seems small, but trust me, it adds up.

Clickteam Fusion 2.5 might be better for you if this kind of problem is unavoidable. I wouldn't know how Game Maker works though, I use the aforementioned CF2.5

No, thanks. I'm making my own SDK.