Like @alexjdale said, using the GUI of the installer app itself will result in an authenticated reboot that bypasses FileVault so you don't have to worry about how it deals with FileVault encryption.
If, however, you have a policy that pushes the upgrade to a Mac, or if you have it as a user initiated policy in Self Service then it does not do an authenticated restart. So it is ideal to have someone in front of the machine, or make sure the user is informed that they will need to log-in through the FileVault pre-boot screen after one of the reboots to allow the upgrade to continue/complete.
Depending on the scenario we've done a mix of all of these things, but the smoothest and lowest risk option has been putting the installer in a Self Service policy that is only accessible to our Deskside team, so that a Deskside tech can facilitate the upgrade and already be present should any issues arise. This is probably not the most practical option if you are upgrading a bunch of Macs at once, but since we mainly do one-offs upon request it is manageable.
