Personally, I was never interested in hunks of rock or meat doing my bidding, having a wisp doing it would interest me a lot more though, having more flashy pretty lights is always better in my opinion, though I would assume lots of others would be sad to see golems go, even if I wouldn't care much.
Though I think you just said they're staying, I'm not fully sure because it's almost 7AM. lol
As for what form you arcane crafting upgrades might take...
Having a structure you build could work, but here's another idea.
Having some sort of machine that'd take up multiple blocks, similar to the weird alchemical thing you'd build with the primordial pearl back in the day (Like, 2X2 wide and 3 or 4 blocks tall maybe?) that's some giant machine that supplies the different upgrades for basically anything that requires them.
I just like the idea of a giant machine with nodes in little glass tube things(Maybe you'd add them in? I dunno if you're keeping nodes or not) and it's kind of like the heart of your upgrading system for other machines too?
I'm kinda just thinking of asthetics, so maybe not. lol