As a coincidence, I had seen your thread yesterday. ;)
Actually, your suggestion there yields an illustration of what is wrong with this system: by the very definition of the median, there is always (at least) 50% of the games that will receive at most the median number of votes. Therefore, it is entirely possible that half of the games get a downgraded mark, even if they were reasonably reviewed.
The only possible situation such that no game receives any penalty is that the 50% least rated games all get the very same number of votes. This is very specific and does not make sense in my opinion.
I have no idea whether itch.io is considering amending the system (which I think they should); you would have to look (in their forum?) if they address this issue.