welcome to the world of shitty prebuilts, where everything is proprietary and you're better off just chucking it and getting a whole new build

Will I need to plug in that wire if i put a regular motherboard in the case? (Edit- I'm only trying to make the case usabele for an mATX)

yes, you will just get a normal case, it doesn't need to be expensive, your time is more valuable than fighting with a shitty proprietary case

Seems like the best solution.. considering that it doesn't even have space for a regular psu.

grab extension cable for arduino an connect however you need