not much difference.
maildir requires 3 (or is it 4?) metadata operations and a file write op
your remarks are mostly true, except concentrates too much on uncommon situations and uncommon strange case of probably tens of thousands of mail accounts that must be very limited.
From my practice mail accounts are at least 1GB large, often 10GB. more often than not other user data is on the same disk.
i've never had more than 50 users on single disk set (which is always 2 disks in mirror), And I/O was never ever a problem except first index build etc. in dovecot 2 you can do this in controller way using doveadm.
Mail I/O doesn't make that much part of I/O for me, still i found a bit speedup by moving dovecot indexes to SSD if it exist.
while disks get larger user data amount get larger too.
Today tape backups are hardly used because it is plain uneconomic today.
most do backups by copying differences to other disk, preferably in other place.
Adventages of pure Maildir format outweights everything else as you have one file -> one mail.
mdbox is something in between.