I looked into this some more and its very odd. When the surnames were combined they became a "double barrelled" name, e.g Seymour Conway. I want to clarify that in this case it was officially by Royal License, but the chances of us finding that are slim (and prob. not worth our time). Non breaking spaces are problematic so the convention was to use hyphens to avoid confusion with other types of names so "Seymour-Conway", or even more fun "Montagu-Stuart-Wortley-Mackenzie". However, the addition of the hyphen isn't actually part of the surname so that's why some sources have them and some don't since they decide its easier/better without it. In the 19th century another trend was the unofficial double barreled name, e.g. my nemesis the Burke Roche family who are all Roche but for some reason a series of descendants had the middle name Burke, which gets written as Roche, Burke-Roche and Burke Roche depending on the source.
I thought one of the peerage sources might have a section on their policy, which the proj. could adopt. Cokayne seems to use hyphens in the Complete Peerage and does not recognize unofficial double barreled names but I never found where he said how he picks surnames to be in caps.
I think I'll just complete the merge since technically both are correct, even if its inconsistent/confusing. Thanks for all the input!