That's why you only use certain ones. I don't use the ones to unlock things unless I really need to (such as me forgetting that you need to do the doors in a certain order and getting fucked over by that). IIRC the only ones that can truly break the game is the unlocking gates and the world level. I really only ever use the teleport and the fluid one (which may not work now cause of the update to them being items...), though sometimes some of the infinite ones cause I have a bad habit of yeeting myself off places because I get tired of trying to path correctly. Oh and the win wild sex one but you can turn if back off, but oh does it make life easier.
The problem is that if you're a veteran player on this game like myself, you come from a time where you didn't had the gates at all. So you started the game, bought the Foxy and Wargy houses, gathered enough by harvesting them to buy the dragons one, then the demons one (Or even reverse those two), along the way you got the Mutt Hut and bam! You had your first Jabberwock Neph, and for that, by doing things the legit way, it would take you a pair of ingame hours as much (And this is if you dont skip things or use cheats like fly back home.
Now however? It takes you still 2.... Entire days, nonstop even for going to the bathroom until you get to the same point. So what do you do to not get stuck in BS? You do the cheat that open the gates, but that creates a whole set of problems, like turning half the NPC interactions pointless, as well as removing things such as the whole Fern progression or having to fuck Neela on each portal to activate them. Among other things.
So in the end you have two hard choices. Deal with the endless grind but having a full content experience, or.... Cutting previously available content for the sake of fun gameplay.
TBH these days I play this game in a lot more of a sandbox way than before, cause at least before the vanilla experience was doable but today without game breaking cheats it's quite the chore so why bother to go on an "adventure" unless you're the one "Minecrafting" your way.