Catch pen confidence trouble: my alpaca always puts himself in the corner

Hopefully this is the right place for this post!

I live on what is considered a hobby farm we have horses, cows, goats, etc. and three alpacas. Recently I added our third boy to the herd he was brokered through the farm I work at and I fell head over heels for him! He came from a farm that uses the traditional corner-grab-restrain method but he has gained a lot of trust for me through using the CameliDynamics approach. It's been amazing to see his progress!

When he first arrived at the farm I work at he was very timid and nervous around people. He had a hard time adjusting to the new environment and alpacas, he and the buddy he came with (who sadly passed away a month after arriving) weren't eager to explore or meet the boy they would share a pasture with on the farm. They were both compliant when it came to coming to the barn to get weighed as well as handling. Neptune (that's his name) would do what was asked of him but he would shut down, I'm not sure how else to describe it; he wasn't participating in what we were doing but he would comply when he was handled. It's like he just learned compliance gets handling over with faster.

He caught on to the escape route and midline catch pretty quickly but was always tentative in interacting with me and other humans. After about 2 months of working with him he began to be more comfortable with me and others working with him. It was fun to watch him discover that I would allow him to make decisions when I was working with him; for example if I saw him get tense I would back off or if I was leading him and he was nervous about something I would let him walk past it at his own pace. As soon as he started eating grain out of my hand it made handling a lot more enjoyable for him, and he became eager to earn something when he was being handled. He started to walk on a lead next to me instead of cautiously walking behind me. Overall he became a lot more curious about what I was doing even if I was working with the other boy in his group.

I couldn't part with him so I purchased him and brought him home! He adjusted so well and super quickly to my farm! He gets along for the most part with our original two boys, they do get after him occasionally but he isn't bothered by it. Neptune has developed A LOT of confidence has become very self-assured. He loves to be hosed down with water and pronks around the pasture in the evening with our other boys. He will come over for grain and eat out of peoples hands when he's out in the pasture, he doesn't have a problem coming up to investigate the equipment when I'm out cleaning. He will even come up to the fence to meet my horse, he's not at all intimidated by her size!

All of this changes when it comes to working with him in a catch pen. Although we have made miles of progress he still gets shy in the catch pen. In the catch pen he puts himself in the corner, I have tried to redirect him out of the corner but he always moves to the next one. He does a little better when the catch rope is around his neck however he still prefers his corner. He also has a hang up when it comes to haltering; he is fine once the nose piece is on but will stick his head through the panel. Once he is haltered he's back to normal, still a little hesitant but he does really well on a lead. I am wondering how to best change this behavior, what should I do differently to change the antecedent? He is very food motivated, I am curious if clicker training would help him be more comfortable in the catch pen. What are your thoughts?