This the the most serious "error" in your understanding. The libraries and core code needs to be recompiled each time you switch destination CPU type or clock speed.
I wouldn't say that's an error. More like a reluctance to type a longwinded explanation. Of course you'd have to compile different libraries for different instruction sets, just as Linux has lib and lib64 versions of many libraries. But compiling/linking for different instruction sets really isn't a big deal. I'll grant that I don't know how much difference there is between the various Atmel processors, but as I only have one board at the moment that's not an issue. I'm also puzzled by your statement that I'd need to recompile simply on a change of clock speed...
It seems that most if not all the complexities could be rather easily handled with a few scripts, which would get me out of the two real problems: having to use the IDE editor, and writing "sketches" rather than real C programs. (It's a lot easier for me to write correct C than to remember rules for "almost C but not quite".)
In any case, we're wandering rather far from my original question, which wasn't "Is this a good idea?" (which I'd already answered to my own satisfaction before the post), but "Has anyone already done this, and wrote down simple instructions?". I guess the answer to the latter is no 
Thanks,
James