In practice no. Petunia (and Trance) try to be as fast as possible. Adding some address translation and trapping of specific addresses (custom, cia etc) to all memory accesses would generate ton of extra code. In any case it would require a lot of work on the actual JIT engine itself. This is unlikely to happen.
To be honest I thought about that a bit more after I posted. However the guys that wrote Petunia and Trance would have a head start over the rest when it comes to attempting this one, methinks.
For any OS component to be usable for GPL application it first needs to be released as part of the OS. Also, releasing such update just to circumvent the GPL license would not be seen as very sportsmanlike I'd think.
I was thinking purely from a technical angle rather than a open v closed source political one.
You know, it's a bit of a pity that the respective operating systems don't provide API's into the JIT that let you build your own emulated 68K based "machine" applications around the OS provided JIT core. I realise there's no requirement for this from the OS point of view, it'd just be really cool to play with.
