Hello @Todd Lazure and welcome to Microsoft Q&A.
So the goal is to merge several files whose collumns are in differing order, and one has more columns than the rest. The mapping, whether default or explicit taking the column order of one file, and applying it to the others, when it should be doing each by name.
I have reproduced your findings. The advertised behavior of default schema mapping does not cooperate with merging files. I suspect when they designed the merge feature, they assumed it would be for merging like files with same number and order of columns.
I have found a way around the comments column. I added in source the "additional column" option, and choose "comments" for name, and give a static, custom value. I found the custom value showed up for the rows which didn't have comments in source. Those that did have comments in source kept their data, and did not use the custom value. However, I found the mismatched data persisted!
I agree this is particularly frusterating. I will report this internally and submit feature request.
I also tried this in Data Flow, and still found the mismatch of data persisted, though it did handle the 4th column better.