Without knowing expressly, I would still say yes.
How is using a smaller cassette (10-40) any different if the derailleur was designed for a 10-50?
So long as the derailleur has the capacity and the spacing between the sprockets is correct, it should work fine. Same as if you used a 10-50 but never actually used the 50

While searching I found this: https://blog.3t.bike/...ram-axs-drivetrains/
I can't imagine the geometry of the mechanical and electronic rear derailleurs would be meaningfully different so it looks like I'm good to go on 11-39 with an eagle rear derailleur.

What lyrrad is pointing out above is that a derailleur made for a 10-50 (or 10-52) cassette moves at an angle a bit differently than the angle of the cassettes you're proposing. The shifting won't be great. Which I think is what you were asking.

I'm assuming you bought the Microshift 12 speed shifter made for SRAM X actuation. Since the cable pull is the same between SRAM's 11 and 12 speed mountain groups, you likely want to pair an 11 speed SRAM mountain shifter to that Microshift shifter instead of an Eagle rear derailleur. Look for an "X-ACTUATION" SRAM 11 speed rear derailleur. Those are made to move in a geometrical path more similar to the 12 speed cassettes you propose. Since the amount of shifts the derailleur does are based on the shifter, it shouldn't have any problem with 12 speeds.

Actually I had one custom made but I just found the one you're mentioning! That would've saved me some cash! Lol! Good call on the derailleur. The old XX1 11 speed was designed for 10-42 so 11-39 should be a decent fit. Thanks!

I would think so. The 10-42 and 10-50 cassettes are basically the same width, so I think you would have better luck with a derailleur designed to be around a 42 tooth at the far edge of the cassette instead of one meant for a 50 or 52. The guide pulley will be closer to the cogs the entire path of travel and be crisper shifting. All of this is just an educated guess though. That 'custom' shifter might be a bit of a wild card too.

Cant that angle be adjusted, at least somewhat?

Regardless, still learning something new everyday around here.

No, that angle is fixed by the derailleur geometry.
Nowadays with the return of the offsett top pulley you can play around with the gap between the cogs by experimenting with chain length as that will pull away or close the gap as the chain length changes.
But usually you only have a single link leeway so you will always suffer shifting to operate the derailleur outside of it's specifications.
And don't get me started about Wolf link and the like, you end up with the top pulley 30mm away from the cogs and they only shift with a new chain.