Motif applications will be built against whatever version motif-config
considers to be the "current profile". Some apps work best with a specific
version, others just plain break with Lesstif (using XmComboBox, f.example).
That's probably not a major problem when emerging an application for the
first time, but certainly is when more than one are updated at once.
Make motif applications listen to a "lesstif" USE flag, similar to "gtk2",
"xaw3d", etc., so even when mass-updating the user's preferences are
remembered per ebuild.
/etc/portage/package.use can be used to store individual use flags per package. see man portage for details.
That's actually what I'm suggesting and also how things worked until late 2004.
Unfortunately, with the advent of "motif-config" there IS nothing one could
put in "portage.use".
If apps don't work with a specified version of motif they should depend on the version that works, they can get the includes and linking flags from motif-config with motif-config -I and motif-config -L.