OK, the new PND is up.
Although this build is not derived from Maquis's build and I don't know for sure how he built UQM, I'm pretty sure the only differences with this new PND are the default controls (set to something more suitable for the Pandora), the categories (Strategy and RPG rather than Action; this makes more sense, and it's usually listed as a "strategy" game in GNU/Linux), the description (I wrote a completely different description), the directory where it looks for addons ("content/addons" rather than just "addons"), and the manual (it explains the quirks of the Pandora version vs. the regular version and is then followed by the normal manual; I don't know if Maquis's PND even had a readme, but if it did, I'm sure it's different), so if none of those changes matter to you (e.g. you have already set custom controls you're happy with), you should be fine not updating.
Note if you update to this version: it looks in a different place for settings than Maquis's build: appdata/uqm/.uqm. If you want to keep your settings from there, just copy the files from the directory the old PND uses ("config", I think) to .uqm.