I'd like to add onto this... while it is true that the awkward structure i'm about to explain is the result of Sega having a Launcher + Client, loads of other games also have this model though rarely do these kind of games release on the Microsoft / Xbox Store. Now, with all due respect, the MS Store (especially its much better upgrade, the Xbox Store) suffers moreso from "good ideas with bad implementations" and does technically work well with certain kind of games... namely standalone games and if say... you aren't interested in the modding scene.
Now the issue with PSO2 is that the MS Store is designed around having updates be done through their platform, not through a launcher, however due to player demand Microsoft mod support had been implemented via a folder known as "Modifiable Windows Apps" which doesn't have the same restrictions as the regular Windows Apps folder. The PSO2 Team essentially used this as a wordaround, the base game (which includes the launcher) is installed through the store while the REST of the game is installed into the "Mod" folder which behaves more like a regular Windows folder compared to the 'protected' Windows Apps folder.
Ultimately the issues PSO2 on the MS Store faces tend to come when you install the game on a drive other than . Whenever your computer restarts the MS Store checks to make sure your games are installed correctly but this check happens fast enough that the other drives on your computer might not even have started. This and bugs concerning where the app manifest expects the game to be installed and its pretty clear that the Microsoft Store version of the game was tested under a very specific environment with things like multiple drives not being taken into account.
The launcher has its issues... but the issues that are directly linked to the way the launcher functions are the same kind of issues that the JP version has (e.g how it has to scan every file prior to patching the game... a file at a time, how the launcher will not wok with IPV6 sometimes, etc). Most of the issues specific to the MS Store version are ultimately... the result of the way the game is configured and how the Store itself works.