Just to make sure we don’t get things mixed up:
While preparing the release of Octave 6.2, an old branch in the MXE Octave repository was re-activated. While the “default” branch is the only one we were using for quite some time, the re-activated “release” branch lags behind with some package updates (I’m referring to all packages, not just Octave Forge packages).
At least right now (and probably always?), you’ll be able to configure and build any of the three Octave targets on both branches. Those are “default-octave”, “stable-octave” and “release-octave”.
In principle, hg branches could differ in many aspects. So, yes, it might be that you’d build different Octave Forge packages depending on which branch you are building from.
But as soon as you selected a branch, it doesn’t matter which Octave target you are building. You’ll end up with the same version of Octave Forge packages.
To sum it up: “branches” and Octave “targets” are different things. The combination of both decides what you are building.
Side note: I’m not sure what you are referring to with “I just edit the Makefile by hand”. But if this means what I think it does, I’m not sure this is a good idea. You’ll end up with an installation mix of two different Octave versions in the same tree. MXE Octave doesn’t even attempt to uninstall a prior version if you just rebuild. (And I don’t think it’ll be possible that one version can cleanly uninstall a different version of Octave.)