I've found a bug in GetFormFromFile.

In summary, the first third-party mod that access a Quest of another mod via GetFormFromFile works.

However, the 2nd (and possibly others) fails.

Read this first:
http://www.creationkit.com/Talk:GetFormFromFile_-_Game

The the below solution and example will make sense:
EDIT: The solution I think to include the Quest Script file (PEX) with the 3rd-party - providing you are permitted.
That file then lays dormant because its ESP is not installed.
It will allow the other third-party mods to work stead than to fail completely.

E.g. with my mods Battle Fatigue and Injuries (BFaI) and Professions, I need to include the Quest for Eat and Sleep (EaS).
With that one file from EaS, neither BFaI and Professions fails.
Without that file, EaS becomes a requirement because either BFaI and Profession fails.

The screens are very confusing. You claim GetFormFromFile is to blame yet your problem seems "No Papyrus Scripts attached". Was that script attached before calling GetFormFromFile? You could test how/if quest C works before that particular function call, is a script language after all. I don't think a fail to call a function will completely unattach a script, yet all is possible with papyrus...