I've just had the same issue. Even if this post is old, here is my suggestions:
1. To run it via command line and generate sequence documentation - mission impossible. The problem is, that it takes for processing currently opened, and active (I mean active on the current tab) sequence file. There is no way to setup sequence path to be processed.
2. It should be possible to modify source code of the tool itself. But, the way how it is done - seems so complicated and strange... We have sequence, which calls dll (generated from the CVI code), which calls sequence file, which has several sequences... I'm wondering, why it is not done as simple processing, using TS API - what can be easily implemented; without this complications. The tool, what should be helpfull for developers - I mean this sequence file documentation generator - is done in a way, that it is not user-friendly... And it is very sad...
3. To solve this task, the best way is to implement own simple tool, which will be run from exe, take input parameters, so the one can start it from the command line.