I had exactly the same issue on my 2017 GS Rallye at 11,000 miles and just after the extended warranty ran out. A small hole appeared in the 'folds' of the rear gaiter. Again my shaft was rusted solid on to the final drive. My dealer tried to charge me to repair it. I told them to fix it FOC as I had dropped the bike in for a final check over a month earlier before the warranty expired and they gave the bike a clean bill of health. The rust had clearly been there longer than a month hence my complaint. They then told me it would not be covered under warranty as the rubber gaiter had a hole in it and they were not covered under the warranty (showing me the clause). I advised Them that the water had got in before the hole as the hole was new, the rust was not. I also suspect the hole was made as a result of it being 'pinched' from the inside due to slight movement from the now seized shaft. I ended up reading the general manager his future if he did not sort it and advised him to request a good will gesture from BMW to sort it. This was eventually done and all parts replaced at no cost to me.
I now have a 2021 GSA and will get the drive dropped and lubbed at its 6,000 service next March.