Indeed even the Kobo issue may not exactly be USB (and thus USB protocol/mode is irrelevant), but purely the system initiating the USB connection and locking the screen without closing the database first. It's a quite strange bug because it seems to afflict certain users, no matter what incantations or OS, other than rebooting. Yet others are fine if they simply make sure the 'home' / 'my books' screen is showing. It also might be that sync has a negative impact and SideloadedMode=true has a positive impact.
I can't see that using MTP or Network USB would stop it happening. It's not specifically misuse of the USB by the host or user, it's a bug in the software that not everyone is suffering, which is no doubt why it's taking time for Kobo to solve it.
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