As mentioned previously, TC dealt with the issue well before the Encore was a thing. But it's all based on the frame, not the barrels.
As mentioned, muzzleloaders that cannot be easily reconfigured don't require ffl involvement in mosy locations. But this thread is about an Encore, that with the removal of a few screws, and the pushing out of a hinge pin, can be converted into almost any caliber you'd like, as a handgun or a rifle. That is a critter of a whole different stripe.
As far as the Remington 700 Ultimate vs the old Remington 700 ML, the Ultimate is actually a short action 700, with a bolt having lugs on it same as a Remmy 700 SPS, Tactical, VSSF, et cetera. The old Remmy bolt doesn't have lugs, or at least not at the bolt face, to engage races in the breech area.
The devil is in the details, as they say.