I highly doubt it's millions. A lot of people here on MR sideload stuff using various methods, but I'd venture to say that the average Kindle user buys their books from Amazon and live happily within that ecosystem without venturing outside of it. Can't say how many who do sideload or use the PDS care about syncing let alone being able to reset it (I've used Kindle's since 2008 and used the PDS half a dozen times in all that time and read many hundreds of sideloaded books). That's not to minimize the issue as I'm sure there are plenty of folks who do have the same problem.
I'd suggest making your feelings known to
kindle-feedback@amazon.com at least it seems to have been a good avenue for change being made to features in the past.