I've done the FCM buy-up multiple times and also used SDC and haven't had a problem with it. They do have to re-issue the ticket however.
Part of the problem is that the original fare basis remains on the ticket, but then there is a separate document number attached to it for the upgrade. On one occasion I had to let an agent know I bought up online to first class because they only looked at the original fare basis and didn't see the linked document.
I'm not aware of any change/difference in policy here. Its a buy up to first class, but the system doesn't reissue the ticket when you do it. It should be treated as a first class ticket. Where you might loose the buy-up is if you cancel the ticket or make a voluntary change outside of the sdc window.