Well, regardless of whether or not it fits into your workflow, I can't help but to accept Canon's own solution to the issue. They are the company that made both the printer and the program after all.
If you're that opposed to flattening the layers before printing, I don't think it would be possible for you to use Print Studio Pro. Rather than any legitimate setting relating to the print output, this seems to simply be a glitch with the software. And while maybe there's potentially some other way to resolve this glitch, I'm sure it would take a lot of experimentation since just by the nature of it being a glitch, whatever solution you find to it won't make any real logical sense.
And to be honest I don't really buy the whole printer profile on a screen method of trying to proof your prints. I admit it's a complicated thing to figure out and I may still have something set wrong, but I've tried proofing on my screen before using a printer profile, and it still doesn't match the actual printer output.
No matter what profiles you're viewing your print on your screen with, you're still viewing it on a screen. If I want to know exactly what my print will look like, I'll just run off a small print for a proof.
Good to hear Canon solved that irritating problem!
The cameras and printers are made by Canon, but then we have monitors, video cards, operating systems, Adobe software, and papers (often) made by other companies. Canon develops a workflow and tech-support methodology that works for them and for many photographers. But I believe Jeff Schewe and many of the printers who share their techniques online have workflow variations that work for a large number of variables.
In other words, one size shoe does not fit all.
In fact, I don't have to worry about whether to flatten my layers: I print from Lightroom. This is the workflow that works for me. I use a Spyder4Pro, and I download ICC profiles for Moad, Canson, and Ilford. The Epson paper profiles are embedded in the 3880's software. They soft-proof with what I consider astounding accuracy.
But I don't print at the larger sizes you do! My largest is usually 13x19.
I'm happily in the Jeff Schewe camp with an Epson 3880 printer; however, as the printer is now six years old, and Epsons's replacement for it, the P-800 seems to have inherited several annoying shortcomings, I am looking hard at the Canon Pro-1000. I don't want to buy another round of ink for a 3880 I believe will need some major service soon. Plus I have a rebate coming if I go with the Pro-1000 and its set of FULL SIZE INK CARTRIDGES. (Take that, Epson.)