Hi Adam
Sorry for the delay, I just saw this post, as Alan's email got buried in my inbox.
I'm not quite sure I follow your question in terms of when the "custom elevation" is pulled from the alignment. Custom is meant to be a user-entered elevation. So can you explain your workflow and how the PRO is behaving differently than a VCL? I just tried on some sample data with a corridor (granted it did not have a 1': 1/2" steps you said, but when I go into the station selection window and select Custom elevation, there's an elevation listed as my "design elevation" which was the custom elevation that was entered in the station selection scree, and that does not change regardless of fixed/random stationing mode. I might be missing something in what/how you're trying to do what you do, so more details about the steps being taken can help figure out what might be happening.
If you'd like to PM me your VCL file I can take a look.