Whilst scanning in full colour would be easiest, blender does have some very powerful abilities to apply materials to individual or groups of faces in the mesh.
In F360 It is fairly easy to split out complex shapes into different bodies for colouring by:
A. Creating sketches from suitable angles - using fit point splines to trace out the shapes of the different colours required.
B. Extrude new bodies from the sketch in each colour to intersect with the complex shape to be coloured.
C. Combine-intersect the new extruded bodies with the complex shape to create complex coloured sub shapes.
D. Combine-cut the new complex coloured sub shapes out of the original non coloured complex shape.
I use this method for putting text or painted logos onto complex ship hull shapes for example, or for applying different colours to organic animal shapes.
See here for better explanation Fusion 360 / BS / AMS Text Workflow - #5 by Ukdavewood