STL files cannot be modified in most CAD programs (solidworks also won't do it). It shows you the part but it is more like a 3D picture of it. You can't even measure features.
I admit, I tried to use OpenSCAD and gave up too quickly.
Using a modern parametric CAD package will let you make a design table to make literally hundreds (if not thousands) of permutations effortlessly. OpenSCAD can't compare to that. The only thing I can think of where OpenSCAD might be better at is if you took input from a website (or other scripting/programming source) and dumped it into OpenSCAD to generate models.
Unfortunately a lot of STLs on Thingiverse are non-manifold or have holes in the surface.
Your slicing engine may produce random results or may even crash if you try to print bad models.
Netfabb Basic or the Netfabb Webservice are more or less the standard for checking and fixing STLs.
You could use the Webservice if you don't want to install Netfabb in your PC.
http://forums.autodesk.com/t5/Inventor-Mesh-Enabler/bd-p/501
You might get an official answer from Autodesk there.