Are you already using the 3D Print Toolbox Addon, that comes with Blender? It has a ‘make manifold’ button.
For overlapping surfaces and many other problems, you could also probably use Booleans.
I haven’t done any (modeling for) 3D printing and I don’t know fusion 360, so I can’t say if that is easier, but I;m pretty sure I could make 3D printable models in Blender.
