Alright I got your holy grail.
This is how it works in Brave Earth. The big trick here is figuring out how handle parallax because for some nonsensical reason, Construct does not calculate that from the center of the screen (I dunno if C2 does this in the not-stupid way, but w/e). Some notes on how this works...
Make your layout big and unbounded. If it's not bigger than the resolution the game is running at the camera gives up on life.
The formula for handling parallax would have to be repeated for different object classes. I kept it to scrolling backgrounds for simplicity. You'd need to make another family to do sprites... which... isn't really a big deal. And you can use this fine with tiles in the gameplay plane and background plane without shit moving around weird.
The higher resolution, the less FPS you get at a rate that doesn't QUITE line up with what you'd expect. For most games you won't even notice though. Kinda an issue in BEP
If you get shimmering with scrolling (Especially if you're like me and end up using a complicated, smoother camera) not related to vsync issues, scroll to your camera's floored X and Y.
I really don't recommend 150 and 250 zooms. 300% onward, 50% zooms become less obvious. Not perfect, but good enough for Shovelknight to run at 1080p.
Besides for weird performance issues in BEP on lower power hardware (in which case, the game can be ran at 320x240 full screened to get max performance), this is the best solution I think you're gonna find.
The only cons here is you get a lot of subpixeling which, depending on how much you care, may or may not be a problem. I don't care about sub pixel positions too much myself, but if you resize an object it will 'break' resolution' in a way it wouldn't at 100% zoom.
You can also use high quality, high res art for the sidebars (and maybe punch out a viewport with the erase effect) and it will show at max resolution which is pretty nice, so you can do stuff like this http://static.gamespot.com/uploads/scal ... 30_004.jpg