How hard do you think it would be to have a 'ZIP customs...' menu item in MegaMek and MekHQ to do that for bug support and other purposes? Identify which of the units that are present are non-standard, and plop them into a new ZIP container?
I did ask about a "zip bug report files" feature at one point, but its a free project and would require some extra legwork to get implemented. And I can certainly imagine there are higher priority things. Its not that big a deal either way, but it is the reason Id prefer the unofficial units remain, if possible.