Two days ago i was working on a page and introduced Panels 3. The page was designed without panels and already provided specific design regions such as the right and left column. So panels was ought to improve the situation...
But then suddenly it came clear there's some mismatch with those two.
If you have blocks enabled - panels will remain in the content part and your ability to modify the whole presentation is pretty limited.
If you disable blocks - panels will take all the space and provide its own rule for presentation. However The markup will still reside on $content ans you need to redo stuff like CSS to make column and regions look identically.
Then there was an idea in my mind.
Why not tagging panels output after panels' rendering with some HTML comments and use hook_preprocess_page to slice panels' $content into pieces and put them in the regions?
Well that's what i did. Added a new layout, added panel HTML comment markers for the drupal regions it provides.
Solution: Perfect theme population, no css tweaks, panels everywhere. Blocks still working. ;-)
What do others think of this tweak?
If this is what you're looking for, we might need a module to simplify this solution (providing preprocess to slice and providing blocks to paste into region).