Ironically, the 39-year-old holds a pilot's licence.
Hall-Thompson was born without a radial bone in his left forearm and had surgery on his wrist to correct it.
"I also don't have a left thumb but my arm and hand aren't impaired," he explained. "On my right, my arm is normal but I've got a slightly crooked right thumb. That's it."
But he didn't have a chance to explain — the cabin manager had already arranged for another passenger to take his place and Hall-Thompson was told he must move.
Sitting next to the emergency exit on the other side of the Jetstar aircraft was a woman aged in her 60s, Hall-Thompson said.
"I'm not saying she was incapable of operating the exit, but if she was then I certainly was too."
The Civil Aviation and Safety Authority also saw no issue with Hall-Thompson's arms, with him previously being issued a Class 1 medical licence.
"If someone is incapable of operating the exit, I understand that they shouldn't sit there. As a pilot, I'm all about safety. I would never sit there if I couldn't remove the hatch."
Throughout the flight, Hall-Thompson said the cabin manager who had an issue with his arm was rude and "deliberately antagonistic", making him feel like "the elephant in the room".
"He came around with the drinks cart and asked the lady next to me if she wanted anything, then went to the other side of the aisle and asked them. Then he looked at me and said: 'What do you want?'
"You feel in those moments like maybe you're being a bit oversensitive, but looking back I think she was being deliberately antagonistic. It was quite extraordinary.
"When I was young, I was occasionally put in similar positions by people but I haven't felt how I felt (yesterday) in a very long time, which is a testament to where society is," he said.
"At first I was a bit angry. To be frank, I was on the verge of tears, which is very unusual for me. I had to stand up and move when everyone had already sat down. I felt like I was put on show a little bit. I was embarrassed. It's shameful."
After the "shocking and embarrassing" experience, Hall-Thompson took to Facebook and his post has attracted dozens of sympathetic comments.
He contacted Jetstar when he arrived home but the whole saga became even more absurd, he said.
"I outlined what happened and the man who took the call said he needed me to agree on a recording that it wasn't discrimination but a procedure.
"It's not for him or me to decide that, but he said he needed me to agree to it for a recording, he wanted to record me saying it."
A formal complaint was lodged and Hall-Thompson was told he would receive a response within 10 business days.
But less than half an hour after news.com.au contacted Jetstar, he received a personal call from the airline's chief of customer complaints and advocacy.
A spokesperson for the airline also issued a public apology.
"We sincerely apologise for Hall-Thompson's experience and are reaching out to him directly," the spokesperson said in a statement.
"There are strict safety requirements regarding exit rows which are mandated by the Australian Civil Aviation Safety Authority, however we are looking into what took place in this situation."
Hall-Thompson insisted he isn't after money or a free flight, but would like Jetstar to explain how it determines who is able to operate an emergency exit.
"I would like their cabin crew to be trained to understand that a physical appearance isn't an overall indication of their ability," he said.
"Something meaningful would be good — to maybe accept that they made a mistake. I would really like for no one to be put in the position I was. It's a nasty thing to do to something and it's essentially unnecessary."
