It's still a bit unclear what the workflow is. Is this all happening in a single session of Fusion or do you expect the cache to be available in different sessions? Also, what in the design are you using to compare the two models; are you just comparing geometry, or are you also looking at features and other information like sketches and construction geometry?
If it's in a single session, then you should only need to read it once and then that document will be available for the remainder of the session and can be used for multiple comparisons. If it's being used in multiple sessions, you'll have to cache the data to disk somehow and an f3d file is the most complete option. It gives you access to everything in the design. If you only care about geometry, it will probably be more efficient to save the model as a .smt file. You can create that either in the UI or using the ExportManager. Instead of using the ImportManager to read it in, you can use the createFromFile method of the TemporaryBRepManager object. This will create the BRepBody in-memory and you can use that do to your comparison.
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Brian EkinsInventor and Fusion 360 API Expert
Website/Blog:
https://EkinsSolutions.com