You have to keep in mind that people may have done something dicey to their devices or that there were some defective units shipped that could account for such reports.
I don't think rooting any miniPC before flashing a rooted or unrooted ROM would be any advantage but maybe Finless Bob will give you a (1000x better) answer to that question. He is the real expert as you must be aware.
I have the Minix NEO X5 so it isn't really comparable but that MK808 is a nice unit. I think they have it running Picuntu already so I'm a little jealous of your stick. Geez, I have stick-envy, gotta get out more.

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