This type of presentation is usually referred to as a 'flipper', and it's hardly new (but, in fact, I fear it will become more common as the industry fights to hold it's obscene profit-margin). A search under Flipper in Doom9 and in other forums will produce many guides and posts desribing the issues involved in a one-disk copy [btw, approximately 70 of the 10,000+ titles on dvd are flippers]. PearlHarbor and LotR-Extended come to mind as real stinkers (especially considering the 9-vob limit in IFOEdit.
The best guides I've seen for transcoding/combining are at:
Check out the whole site/links--but the one most relevant is the one for LotR (these are compiled guides, well linked to other common ones...).
Tip o' the Hat to SirScrub.
edit--btw, these 2-disk flippers (inclusive of the side A/B variant) are common enough that Sony mega-changers are built to handle their two-sided nature during playback...puts me in mind of old Wurlitzer's!