First of all, the copyright holder of "real" custom software is the company
that pays for its development. Since it is the only user, there is no
redistribution and no need to talk about licensing.
If a third-party developers retains the copyright (in the hope of selling the
same work to another company: not that "custom"), then she should deliver the
work under the terms of a free software license. Otherwise, she subjugates
the user. By attracting the user with a free software barebone version of the
proprietary software, she somehow fooled the user in the first place. And no,
no reasonable user prefers the software to be proprietary rather than free
(who prefers to potential run malware?, to not have the ability to contract
anybody to fix a bug or further develop the software?, etc.).
The free software license can be the GNU GPL. The GPL, like any free software
license (by definition of free software), does *not* force anybody to
redistribute the software. Even after modifications. Freedoms 2 and 3 are
freedoms. Not obligations. What the GNU GPL (and any other copylefted
license) does is to guarantee that the original author will never see her
work subjugate users. Indeed, and if they happen, redistributions of the
sofware (modified or not) must be done under the original license.
Finally, you seem to oppose "commercial licensing" with "GPL licensing". This
opposition does not make sense. Many companies make money with GPL software.
Including through selling custom modifications, the topic of your post. The
FSF even encourages "people who redistribute free software to charge as much
as they wish or can"!
