Hi @FrustratedElectron. Thank you for looking into the project. I would love to see ptychography implemented.
As you have already discovered, the source design is in OpenSCAD, and the solid parts are STLs. OpenSCAD uses a constructive solid geometry approach to CAD, which is fundamentally different from programs such as Fusion or FreeCAD, which use constraints based geometry. It is not possible to make direct conversions between these different approaches.
There is some explanation of the reasons for using OpenSCAD in the first place, and the consequences of that, in Alternative file options other than STL for block/delta stages? - #2 by WilliamW .
If you are wanting to make significant modifications to the main body, you would be best working in OpenSCAD. If you are wanting to modify accessories, or things that mount onto the optics fitting or the illumination dovetail, then these relatively simple parts do not take too long to recreate, or you could try the methods in Towards STEP components . This should work for most of the mounted parts. You might only need the part that mates to the OpenFlexure mount, from there you can add what you need.