I've spent some time looking into this issue. I apologize for the delay. I cannot seem to recreate the problem.
I've gone through and tested the
get_the_term_list function with both built in and custom taxonomies. It is displaying the proper order in my setup. With that said, I could see a situation where the sort might not be displayed. It would only happen in a very rare circumstance, one which I could not even create when I was trying. That said, I did apply the sorting algorithm in another place to try to catch when this situation arises. I just updated this and it should be available to download from the WP repo/available for automatic upgrade within 15 minutes.
The biggest problem here is that I could not create the problem, so it is hard for me to know if I fixed it. Please let me know if this fixed your issue. If not, let's talk some more so I can try to get this sorted out.
Thank you so much for your feedback!