Configure correct NNJVT properties for HLT in python

@wbalunas pointed out that we were setting the wrong config file paths as there are two sets of properties toggled inside the tool based on another flag choosing the set of input variables.

In this case we were saved by the fact that we are just setting the default values so all that happened was that the python made the irrelevant configs identical to the defaulted ones actually being used.

@dwilson this is a reason we may be better off consolidating the input file properties, and leaving all the switching to python.