You wouldn't have to do anything different as long as the rifle barrel is long enough that the firearm would not qualify as a short barreled rifle with it installed. If the rifle barrel is short enough that the firearm would also qualify as a short barreled rifle with this rifle barrel installed, then you just list this detail on the ATF form, and list the firearm as an SBS/SBR instead of as an SBS. In other words, on ATF Form 1 in the description section (4), you would just print 'short barreled shotgun/rifle' or 'short barreled rifle/shotgun' in box 4c, and then in box 4d you would print both the gauge of the shotgun barrel and the calibre of the rifle barrel. In any case you would only need to do, and could only do, a single NFA registration, because for any particular receiver (the only part the ATF considers to be the firearm) the ATF only allows one NFA registration at a time. For example an M-16 with a 10 inch barrel could only be registered as a machinegun, it could not also be registered as a short barreled rifle.
The main point is that if you are registering a firearm as an NFA weapon, and plan to use it as a multi-cartridge platform, it is a good idea to list all the calibers you plan to shoot out of it on the ATF form. Of course you don't have to worry about listing calibers you think you might someday shoot from the firearm. Even the ATF doesn't expect gunowners to be psychics who can see into their own future (the ATF just expects gun owners to be psychic enough to see all future ATF rulings
).
You could probably also register this firearm as either just a short barreled rifle or as just a short barreled shotgun, and then list a single caliber/gauge in box 4d, since in either case you are listing correct description information for the firearm. However, in this particular situation there is no disadvantage in providing the additional information on the ATF form, while there is a chance (however slim) the ATF might call foul if you don't provide all the caliber/gauge information you were aware of at the time you filled out the form. Of course unless they read this exact post there isn't anyway the ATF would know better, but again there is no disadvantage in providing the additional information, so you might as well.
There is an example at
www.titleii.com of a ATF form filled out in 1976 for a similar situation. In this case it was a transfer between a gunowner and a class 3 dealer, so it is Form 4 rather than a Form 1, but the description sections are identical in both forms. It is at:
http://www.titleii.com/BardwellOLD/pdf/4_1_75.pdf
This particular example is also interesting because the firearm in question was an old Marble Arms combination gun, and it was transferred/registered as a short barreled rifle/shotgun rather than as an AOW, even though AOWs are what combination guns are usually transferred/registered as.