Hi Chris,
This issue is a known limitation on Revit 2018. It was fixed in Revit 2019, where users are able to create\select individual objects from inside the steel connection. In Revit 2018 the steel connection geometry is one object, in Revit 2019 the users are able to select the individual object and thus select the base plate as an input element for the "Gusset plate to column and base plate".
The name of the steel connection makes a little confusion. It's called "and base plate" but it works on both Beam or Plate input. It was added to Revit 2018 because a user can create that connection between a column, a Beam (as additional object) and a brace.
As I mentioned earlier, in Revit 2019, the additional object can now be Beam\Plate object.
Regards,
Mihai Sandu
Sr. QA Analyst