Bus429, I have had regular upper endoscopic examinations for the past 6 years. About to have another one in a few weeks. My very first one involved the throat spray which is very bitter but otherwise okay. But, must admit I am pleased that these days my hospital's protocol is to use the full twilight anaesthetic (Midazolam + Fentanyl) and you're asleep. No need for "swallowing" the scope. Procedure only takes about 15 mins including taking biopsies, might take a little longer if they opt to repair anything they can whilst down there. You wake up in recovery, the nurses monitor you closely (BP, temp, etc etc), they get you up and once you can eat they feed you. It is a very comfortable procedure if a little strange. The hardest part I found was having my jaw opened so wide to bite down on the mouth guard (so you don't bite down on the scope during examination!).
If you are a bit nervous, just mention that to the admitting nurse. I have always found all the doctors and nurses to be very reassuring, they want you to be comfortable.
As for reflux/GORD/GERD having an impact on aviation activities, here in Australia the DAME (aviation medical examiner) needs to make an individual assessment. Most PPIs and H2As don't prevent you from flying but your doc needs to look at the whole picture.
Good luck!