Those are some serious questions.  Have you asked your Sage Partner yet?

The MAS90 folder contains files related to the system, beyond the data (like the data dictionary, SQL server location and credentials...) and some legacy settings like ALE lookup files.

The migration tool handles all the additional settings within those MAS90 system files which would be practically impossible to do manually.

I have not. I have some issues with our reseller due to a non-sage related event. 

So basically, do the sage file system restore, then sql restore. Start Sage and all of the data from the last SQL backup will be present? Or do I need to reinitialize the datafiles in Sage? 

Make sure your system backup is recent enough to contain any system changes.  If you added / edited a UDF after the system backup, the database could be misaligned with the databases.  Same with installing product updates / enhancements... you need the system files to align with the SQL databases (which include all databases starting with MAS_... always copy MAS_System along with your MAS_### company databases).

But this is just general advice.  You should really talk with someone familiar with the specifics of your system to get a more detailed analysis of your B&R strategy.

File system backups are taken every hour, sql backups every 30 minutes or 1hr. Very little going on in the way of changes to enhancements, UDF's, etc. But basically, if any of that happens, I'll need to restore to an older SQL backup. 

No reinizialtion should be necessary in Sage? 

What do you mean by reinitialize?

Disaster recovery assumes you have tried the process and verified it works.

I had a false server issue and I put my disaster recovery in to action. My sleeping instance told me I couldn't update the subscription as the AMI was no longer available in the Marketplace. Trying to restore the nightly backups failed with bad signatures. It seems the software I was using to do the auto backups was uploading garbage to S3.

Thankfully the issue with my server was my IP was jailed by the hosting software preventing access. Once I made the IP trusted everything returned to normal.

I spent the rest of the day certifying my disaster recovery worked and not just assuming it would.

Agreed.  Testing the restore is a critical part of any backup and recovery solution.

library maser \ utilities \ reinitialize data files || rebuild sort files || etc 

Yeah I should probably go ahead and export my test environment after making changes to it (invoices or whatever just to create some delta between sage and the database), then reload it - which is what I would do from DATTO restore. I'm not super concerned with the database restore - I'm comfortable with SQL restores. 

Reinit = delete all data in the table.  Don't ever do that for any table unless absolutely necessary.

Rebuild Sorts = safe but should not be necessary.

Some service / session control files may need to be rebuilt, but you'd get error messages if that is needed (with instructions in the Sage KB).