Stuff like exclamdown was auto-aligned to x-height in G3, just opening this file in G2 shifts them to cap height. I suspect it’s because G2 auto-alignment is not as flexible? What can I do to prevent this behavior?
Why do you need to open it in Glyphs 2?
You can disable alignment before you open it in G2.
But I want automatic alignment 
Is there a way for G2 to ignore vertically shifted auto-aligned components?
No. That is new in Glyphs 3.
You need to disable the alignment for components that move. You can use metrics keys to get close to auto alignment.
But still, why do you need Glyphs 2?
I can actually get work done in Glyphs 2 
Can you give me the most important issues that prevent you from working properly in G3?
My post history documents it pretty well, I guess The bottom preview not centering is super annoying. Also the stroke popup obscuring alignment buttons. And kind of new, a fun bug with RMX where only nodes are shifted but not the paths in the preview.