As an opening, a big thank you to all those who release mods (whether converions or new content) for TTW. It really does build community spirit as well as the obvious MOAR STUFF IZ FUN.
However, the GECK is not perfect, and every so often stuff happens. The only reproducible thing I've personally found is some cell and worldspace records (which seem innocuous) which ALWAYS get saved, but I'm sure there are other such instances.
Mostly though, there are a lot of people (or at least it seems like it) who are unfamilliar with FNVEdit, and who, consequently, may have trouble if Generic Mod A has identical to master records but loads late and ovewrites actual changes to earlier mods (which is the whole point of cleaning, really).
If you can make a mod in the GECK I feel pretty confident in saying you are knowledgeable enough to clean it with FNVEdit. MOST (probably something upwards of 90%) of the plugins I've grabbed from the forums here have been clean (bar a couple with those annoying cell and worldspace records) but since no-one knows a mod like its author, it would be good, I think, to make sure you clean before you release a plugin, even if it's miniscule (like a 3 record compat patch).
Anyway, that's that.