Increasing Microsoft Graph Per-Mailbox Throttling Limits (PUT/POST/PATCH & Concurrency)

There is no straightforward answer to this as a lot depends on the specifics what you are doing and how often it occurs. It also depends on the size of the tenant and the other things that are happening within that tenant (at Graph level). For instance, is this a continuous thing, is it in bursts is it for a migration scenario?

Also, are there other ways of doing this which wouldn't exhaust your endpoints? This isn't just about optimizing your Graph calls, but also looking at (native) alternatives such as Power Automate.

The best way to go about this would be to contact your TAM at Microsoft and also create a support request. If it is actually for your customer's tenants, have them do the same thing. Valid use cases are usually considered, and you might even get some tips along the way when working with the correct engineers.

If this is about data extraction, consider Microsoft Graph Data Connect as an alternative;
Microsoft Graph Data Connect overview - Microsoft Graph | Microsoft Learn