Bruno,
I suspect the documentation for the NASA spreadsheet was written somewhat informally, I would not apply the most strict interpretation to their words.
Typically form factors account for form drag. Form drag is a pressure drag -- but that is viscous in origin. It relates to the thickness of the boundary layer at the trailing edge. While it is often treated as independent of lift coefficient, a more thorough analysis will reveal that it is actually a function of aoa or cl (even in 2D). If you look at the data in Theory of Wing Sections, you see largely parabolic behavior for 2D drag data -- it is not induced drag, but lift-dependent form drag, which is a viscous drag.
VSPAERO has a simple form drag model in it. It is based on some empirical data for NACA airfoils. It is sensitive to local Reynolds number, thickness to chord, and local lift coefficient for wing-type bodies. It is sensitive to finess ratio and Reynolds number for non-lifting bodies. You will see it output as a separate term -- the term can vary with lift coefficient.
This calculation will only include contributions of components included in the VSPAERO Set. So, if you throw out some components, they certainly will not be included. This model can do a good job -- particularly if you have a wing with a lot of taper (large Reynolds number variation) and other things like that. I really like it for rotating wings -- it is the best way to get a parasite power contribution on props and rotors.
OpenVSP's Parasite drag tool uses form factor and wetted areas to do a traditional drag buildup. The user can select their preferred method at every step of the way. The user can also input interference factors, etc. There is an additional sheet for including excrescences. The lifting surface contribution is not a function of alpha (cl).
I see these tools as complimentary. At a minimum, you could use VSPAERO's inviscid induced drag term along with OpenVSP's Parasite Drag tool for a simple buildup of the remaining drag. For an aircraft with props and/or rotors, I would suggest using the VSPAERO parasite power. Then, as you want, you can include the VSPAERO parasite drag term and replace the corresponding terms from the OpenVSP drag buildup.
As always, these things take engineering judgment and some experience.
Rob