This is due to MM's encryption enforcement. You'll really notice such but this shouldn't be all the time when you restart the phone. On what trigger to have the encryption cause boot delays, it's non-conclusive. Can the encryption be turned off? Yes, but not manually. You'll have to trigger the so-called "FRP" and use the same account of course. I've done this 3 times and my AF2 turned out to be decrypted under Settings > Security - only milliseconds added to boot times, similar to LL.
Only encountered on SD set as Adoptable that usually does require a restart specially if getting the "Unfortunately, " message.
Mine was flashed via both update.zip and flashtool, by the way, and not much difference on both way when it comes to experience.