Ok so here is a work around for some that can do so, those experiencing this issue with Windows Store Version of PSO2 you can use the newly released Steam version of PSO2. The icon will once again appear on Window 10 2004 Taskbar, etc. while launching and playing the game through Steam. Keep in mind this is not a solution for the Windows Store install so take it with a grain of salt.
I still hope that one day they will solve the windows store issue, till then i say this would be a solid work around for most.