At stage 5) grub writes directly to HDD, omitting the raid1 level, so /dev/sda1 and /dev/sdb1 become out of sync and weekly cron job 99-raid-check complains about mismatches.

Suppose I memory-map a file and often modify the mapped memory. The system will at some point decide to write that block of the file to the device. It will send a request to raid1, which will send one request each to two different devices. They will each DMA the data out of that memory to the controller at different times so they could quite possibly get different data (if I changed the mapped memory between those two DMA request). So the data on the two drives in a mirror can easily be different. If a ‘check’ happens at exactly this time it will notice.

Normally that block will be written out again (as it is still ‘dirty’) and again and again if necessary as long as I keep writing to the memory. Once I stop writing to the memory (e.g. close the file,
unmount the filesystem) a final write will be made with the same data going to both devices. During this time we will never read that block from the filesystem, so the filesystem will never be able to see any difference between the two devices in a raid1.

So: if you are actively writing to a file while ‘check’ is running on a raid1, it could show up as a difference in mismatch_cnt. But you have to get the timing just right (or wrong).