Doing the following in pkg_setup() # If both enabled, use gtk+ only ${use_gtk} && ${use_motif} && use_motif='false doesn't work. You depend on gtk, but don't store the dependency this way. I'd say using only the gtk flag, to avoid invalid flag combinations would be the easiest solution here.
For 3.1, we've fixed this already, Motif support is being phased out. For 3.0.x, it should theoretically be possible to have both Motif and gtk+ enabled at the same time, but our ebuild just doesn't support. If somebody wants to clean this, they're free to provide a patch.
Now that 3.1 is final and soon to be marked stable, I hesitate to attack this problem, since 3.1 is a massive improvement over 3.0 and (it says on the label) 100% ABI backwards compatible. In 3.1, we dropped Motif support as promised, so I'm closing this. If there are severe objections, and a general feeling that we should fix the 3.0.x series here, please reopen.