there is a completely GPLed packer, called upx-ucl (the one that you get when you compile UPX and UCL from source). It packs slightly weaker than the precompiled upx (upx-nrv).
In Tom's comparison, for FreeCOM (~93000 bytes uncompressed) upx-ucl ~ 67500 bytes upx-nrv ~ 66000 bytes apack ~ 63800 bytes
But you already wrote that since the STUB is the same, UPX-NRV *can* be used too - and you do it.
All that needed is a special exception clause to the GPL to clarify (with agreement of all copyright holders). However that makes the utility GPL-incompatible so it is no longer possible to copy/paste from other GPLed sources without permission from the copyright holder.
The kernel has many contributors (copyright holders), so it'd be practically impossible to obtain permission from all of them, but most other software has only a few or just one, so anyone could change their license to something less troublesome. (I don't think that this would happen though, so please don't blame me that I'm provoking heresy here ;-)
Lucho
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