You can easily use seamless branching on the originals. I don't see why that's a problem at all. Of course, everything would have to be color-corrected to match (hopefully the SEs to match the OOT).
I'd rather have the SEs be seamlessly-branched together, but have the original versions on separate discs, mainly so I can throw the SE discs away entirely like I did with the GOUT. But I don't see why they couldn't do seamless-branching if they wanted to.