I'm trying to replicate this, but couldn't. I don't have a Cargo airplane installed in P3D, but it doesn't really matter, I flagged the A321 imported from FSX as Cargo airplane, so it's exactly the same (you can see it has Cargo Stairs now), called Boarding and have all 3 characters, two pilots and one Loadmaster, see the attached screenshot.
From your log, it seems the LVar GSX sets up for 3rd parties to control this was set to a non-zero value, as indicated in this line:
"Add-on or User decided not to board Crew"
Which comes up if that variable is non zero. GSX never sets it, it's reserved to 3rd party add-ons to override GSX's behavior so, if you have that line, that variable wasn't zero. I'll post an hotfix with more diagnostic info, so all these LVars wil be printed if they are not zero, which is GSX default condition.
Also, please clarify how the "Ignore crew on boarding" option is set in your main GSX Settings page.