Hey,
on the systems I know (Arch Linux, Debian, Ubuntu) that offer multiple Qt versions concurrently the binaries are postfixed with a version number. On Arch there's qmake, qmake-qt5, qmake-qt4 with qmake being a symlink to qtchooser (which supposedly choses the correct qmake version for the project you're working on).
On Debian there's /usr/bin/qmake, again a symlink to qtchooser. The actual binaries are located in /usr/lib/${host}/qt5/bin/qmake (dito for Qt4). No real guidance there.
Arch's method seems useful to me: install symlinks as ${MXE}/usr/bin/${host}-qmake-qt${VERSION}. Whether or not it makes sense to include qtchooser with MXE somewhow is not exactly clear to me, so for the time being I would suggest not to install version-less symlinks (${MXE}/usr/bin/${host}-qmake).
It would be nice to have the other tools (uic, moc) linked like that as well, but as you've pointed out already that qmake's capable of locating the correct executes itself I won't insist on it.
I can whip up patches for MXE's build files for both systems once we agree on a scheme.
Kind regards,
mosu