If you restore the backup on a new phone, you'll have to resync all desktop machines, and at least on Windows syncing old messages has never worked for me.
Also, considering that linking requires access to your existing device I don't see an issue with that. Moxie himself considered usability to be more important than tinfoil hat-level crypto because large-scale adoption is what enables security.
The limitation is that only message history from the past 45 days would be synced. If this has changed recently to allow syncing all message history, I’d be thrilled!