Sure you can modify it, but only trivial things like scaling, chopping of a part, and if you are lucky, meshing it with some other part, will be easy.
Say for instance you want to do something simple, like use another sized tuning pegs for this violin. That means changing the diameter (and possibly depth) of the holes they go into.
In any reasonable parametric CAD software model (as Fusion 360 enourages), this is merely finding the sub-part that represents the peg or peghole, and entering in a new value for the diameter - every affected area of the model will be updated, correct & still manifold (watertight).
With an .STL you will need to find & select all the relevant edges/vertices for each hole, and nudge them around until they (hopefully) fit.
This is a trivial example, it becomes more interesting (more painful) if the feature at hand is more complex. Say if there was a trapped nut.
In an STL, all the humanly meaningful parts of why the model is the way it is, how it is built, is gone.
You can dissassemble some executable you get too, and muck around with the code to do modifications - but its hardly how one should do open source.