The purpose of the move is to limit the “webapp loophole”, where you could sell access to a modified version of a GPL product, but not distribute the changes.  As Ivan put it:

“I want Freeside to be free for everyone to use and modify, but I don’t
feel it is equitable to our community for large companies to fork
private versions of the software and sell access to them in a
hosted/SaaS/ASP capacity to avoid having to make the source code of
their derivitive works available.  This seems to violate the spirit of
the GPL and copyleft, if not the letter (hence why it is called a
“loophole”).”

The purpose of this is not to block customized code, but only selling out usage of non-contributed code.  This will not prevent the development of custom plugins, which the Freeside architecture encourages, but only selling hosted access to those. 

Interested parties are invited to particpate in the AGPL draft discussion: http://gplv3.fsf.org/agplv3-dd1-guide.html