I'm beginning to think that it is something that the mod author has done wrong vs it being skyrim itself. Here are 3 mods I'm using now that contain quest and all seem to work together without any of the problems stated in the OP.
http://skyrim.nexusmods.com/downloads/file.php?id=9782&navtag=file/images.php?id=9782&tab=3
http://skyrim.nexusmods.com/downloads/file.php?id=17289
http://skyrim.nexusmods.com/downloads/file.php?id=8333&navtag=file/images.php?id=8333&tab=3
So everytime I install a mod with a quest in it I do hours of testing for stability purposes. So with these three mods I seen no side effects. I'll test my luck and continue to add more to see what works and what doesnt.
Please do, I can list some quests, but seeing your load order would be a big help.
http://skyrim.nexusmods.com/downloads/file.php?id=15896 (Can run this as an ESP)
http://skyrim.nexusmods.com/modules/members/index.php?id=3013861 (Could run 1, running others resulted in instability and Sea of Ghosts is a huge ESP which I could not run till splitting it and placing his custom worldspaces in an ESM. Splitting all 4 quests allowed me to run them concurrently without "specific" CTDs I observed with them)
http://skyrim.nexusmods.com/downloads/file.php?id=15126 (WIP, the quests are non-functional, but still did not run for me unless split)
http://skyrim.nexusmods.com/downloads/file.php?id=14971 (Curiously could run her other dungeon, 'Onyx Caverns' as an esp)
http://skyrim.nexusmods.com/downloads/file.php?id=12935 (Could not run as an ESP)
http://skyrim.nexusmods.com/downloads/file.php?id=16197 (Another no-go ESP)
http://skyrim.nexusmods.com/downloads/file.php?id=17246
http://skyrim.nexusmods.com/downloads/file.php?id=16810
By no means am I insisting you download and give all these a go, I usually test any reasonably decent quest/dungeon I see on the Nexus. These are just what I have as ESM+ESPs at the moment.
So using TESVSnip at all will cause corrupted entries? or only if the esp/esm contains the mentioned record types?
I am wondering this as well, I have split a number of ESPs with TESVSNIP and occasionally encounter holes in the dungeons I test, all is well when LAL is removed for the most part (Sometimes the dungeon/quest split just doesnt cooperate [I haven't actually been able to keep Live Another Life enabled and not have holes in Chillwind Depths and Nightcaller Temple with my current load order, I assume the behavior is the same with the UKSP]). I imagine this is a result of using TESVSNIP. Definitely not blaming LAL or UKSP here, just reporting what I've observed! Looking at TESVGecko's indefinite release date, I assume we have no alternative aside from the CK at this point?