This STILL screwes me up in ZBrush.
I can think of only one reason for things to not work like you are describing, and that is Adobe claiming they invented the way layers work and backing them selves up with lawyers.
The problem with the ZBrush SubTool Pallet is it LOOKS just like the layer thing in photoshop and a million other programs but it does not WORK like them at all, just the way the Eye Icon works makes it a miserable experience even with only a few subtools.
The things you are making, the museum shots and framed pictures are stunning and you mentioned a MaxResize Script, what is that? It sounds very cool!
You mentioned photoshop actions also and I think that you CAN do stuff like that with ZScript, by recording stuff and running it later, you can even (Talk to Marcus about this) make it happen over and over if you want.
Also are you actually printing these?? Post number 462 is freaking me out…