Hi!
I think what I've realised is that there is no real answer. I think I was in some way confused about both things you mentioned even though as you said, the first one isn't an issue, I was just kind of misunderstanding/overthinking some things.
What I realise now is that while I can have everything made on the same size canvas, they'll then all be the same size proportionally, which obviously doesn't work. I did find a bitsy-like program that I really like the UI of as it makes sense to me and isn't overwhelming, and I like the options it has (it's called Whimtale, formerly Whimsy) and in messing around with that I've gotten a better idea of things because I could see it in action.
I didn't actually go through with the process of importing into Bitsy, but had found a hack for it.
My issue now is trying to figure out what the right ratios will be. Obviously to make proportions seem right, my avatar needs to be made at a different size from the other assets, like a column or the displays on the museum. Which I've seen can be made using more than one canvas and pieced together, like taking up one whole 16x16 canvas for half a column, and another for the other, then stacking those to make the column. That is helpful, but now I still have to figure out what my base is going to be and how to get things proportional from there. It seems the first place to start should be my avatar, figuring out how big that should be, and then how big the whole "room" or "scene" should be, and then the individual assets so that everything makes sense and doesn't look like the character is too small or too big compared to other things. That's ultimately where my problem lies now.
Thanks for your reply! This was actually really helpful especially since I saw it after messing around more and getting a visual to some of this so I could better understand what it is I need to know and what I have to work with.