the rebooting is not the problem, i do it once a week and delete magisk app stubYup, Magisk daemon will restore (rebuild) Magisk config files on bootup if deleted, and has similarly, for some time now, detected if Magisk app is missing and restored stub app at boot time if necessary.
In recent months I've noticed this has stopped functioning (removed / regression?), and I actually searched to see if it was removed on purpose... Couldn't find a commit, so guessing it was a regression, and it has been fixed or reinstated again here in any case:
Install stub if necessary
(topjohnwu committed 7 days ago)
So sorry, this is a feature, but I wondered myself if it is really necessary for the same reasons as you... I don't know how it can be easily bypassed... PW
but now every time i run an app with root access the stub appers without rebooting my phone
and some banking apps didactic that my phone is rooted