It cuts to the core of what we actually want from free software

Mostly people want free as in beer and actual users of Audacity use Audacity because they want to process audio.

it does make me slightly uncomfortable

Then you have a choice to make. There are many other audio software packages with a variety of tradeoffs to choose from because everything is not for everyone.

make money for Muse Group

To me the strategy appears to be that strengthening the two open source projects (MuseScore and Audacity) enhances their many commercial offerings…for example a stronger MuseScore is better for Hal Leonard Publishing particularly in light of the demise of Finale and a better Audacity code base is a good way to develop the audio code that other Muse Group products need anyway.

And for what my pure speculation is worth, the purchase of the trademarks for Audacity and MuseScore could rationally contain conditions underwhich Muse Group would have to sell those trademarks back to the original owners.

But even absent such conditions of sale, the original trademark owners likely trusted Muse Group to do the right thing (and if the sale was just about money, then the original trademark owners were already mercenary themselves and so whatever trust you previously had was already misplaced).

While the codebase is open source, the website could provide binaries that were not built from the open source code (e.g by patching to add tracking).

That is a violation of GPL.