I haven't used git, so I won't try to answer in git terms. Think more like a RCS repository, with no fancy distributed system. Each one of your clients checks out a tree, makes changes, and commits the changes back to the central repository. You don't get the changes made by another client until you do a sync. When you switch from MobileMe to Bonjour, you are taking your tree (which has no version history) and establishing a brand new repository, but you don't get to have any history of how you got to that point.
"Keep device" takes what you have and makes a new sync database from it. When the Mac (or another iPhone/iPod) goes to sync, they will detect that the new sync database is no longer compatible with theirs and ask the same question. Assuming you intentionally replaced the sync database, you would tell them to take the sync database.
If you have some sort of cock-up where devices get out of sync and you have changes on more than one that you need to save, you can use this same behavior to your advantage. Go to the first device, and tell it to replace the sync database ("keep device"). Go to the next device, and change its configuration to sync to a different path (if using MobileMe/WebDAV -- it's a bit more complicated to describe what to do for the Bonjour case, so I'm going to be lazy and not do so as you don't actually have a problem). Then tell it to sync, which will write a copy of its local database to that new spot. Repeat for any other clients, using different paths for each. Now you can go back to the devices which saved their changes to new spots, configure them to sync to the usual place and have them do so, keeping the sync database. Finally, copy those extra sync databases to the same Mac, double-click each one, and drag and drop or otherwise duplicate any changes that you need to rescue into the main database window.
Yes, it's a limitation, but it's far from obvious to me that removing the limitation is worth the effort, considering all the other features the developers and the users want added. People who aren't going to use that functionality (probably the vast majority) will squawk if any new bugs are introduced into their sync functionality, and the people who want some other feature which doesn't get done because the needed engineering resources went to this won't be happy either. Impossible for us to know whether the forum traffic is proportional to the requests made to the support ninjas via Help->Send Feedback and email to
omnifocus@omnigroup.com (which are the feature requests that actually matter), but number of people I see requesting this feature is small compared to a lot of other features of seemingly comparable difficulty. If it's really important to you, send in your feature request as above...