I'm putting together a puzzle that requires multiple Keys and Reject Keys for the same slot, however I tried to click and drag to select them all, as well as Ctrl click to try and select multiple, but neither worked so i'm having to select them one by one.

Is this something that can actually be done but i'm doing it wrong or is it not possible?
And if it's the latter, could it be a functionality that's added in the future?

Well shift click is how I select multiple things. But idk if that works for what you're doing cause my brain small.

You can do that, but you have to do them one at a time. I've done this for a few puzzles already.

also, just a thought, but would it worthwhile colour coding the lines to each key type?
At the moment, the lines to both Key and Reject Keys are red. If you are using the same item type for both Key and Reject it's hard to discern which is which. (I'm using plains with different textures to create different items, however the thumbnails in the properties menu do not reflect the texture applied, hence it's making it hard to work out what i've done.)
Perhaps making the Key indicator Green might help?