@Marc ********
This is something I have seen several times at the Samui office, which is one of those renegade offices like the one on the Island of Misfit Toys (aka Koh Phangan)
They make you take the 30-day extension on your free stamp entry then they let you apply for the 90-day Nom-O.
Then they tell you do not come back until that 30-day extension expires because that's the day they will ink in the Non-O visa and give you the new 90 day stamp.
Dial the paranoia back just a notch or three :). IF they took your documentation, took your 2000baht, did the home visit, you aren't going be be denied and won't be in a "massive jam".
I have never seen someone whose application for an in country Non-O visa was accepted by immigrations (paid and got a return date) who was subsequently denied the Non-O 90 day visa.
You'll be fine. just wait it out..