Based on other boards that use MicroSD cards for the OS, sometimes you have to be careful to select a good quality card. At times, some MicroSD cards work fine for casual use. But, an OS that gets monthly package updates and is used for actual user logins, some SD cards won't last as long.
It's probably too late for the current BeagleV board, but I would suggest a eMMC slot / socket, similar to what Pine64 uses. That allows the user to skip the eMMC if they are happy with a MicroSD card. Plus, a motivated user can get 128GBs easily and 256GBs if they try harder. Of course, eMMCs are expensive, but are intended to last much longer than SD cards. (It also helps that eMMCs can be noticeably faster than SD cards too.)
On the other side, if it's easier / cheaper to have a single SATA port instead of a eMMC port, that would work too. While SATA DOMs are not cheap, they are an option. Plus, if the socket is powered for SATA DOMs, it's pretty simple to plug one in. Though, a board supplied 5volt power jack should also be supplied, (if supporting SATA DOMs).
And if the user does not want a SATA DOM, they can use a plain SATA disk or SSD.
Basically something more reliable for storage than a MicroSD card. (I do not consider most USB flash drives as reliable... they tend to be as reliable as MicroSD cards, as in not reliable.)