Strange. Glad you were able to trace it and get some clarity. Sounds like an unused part of a previous system as you said and the drain included a vent.
If the top and bottom/exit are capped, should be able to remove.
The vent could be re-purposed especially if you wanted to do a composting toilet.
At least with my van, the SMB documentation is really generic not specific to my build except for component manuals.
2008 GMC 3500 Quigley Weldtec 4x4 Savana SMB