John,
I have used FreeCAD a lot, but I do not generally import STEP files. There are numerous options in the preferences for STEP import, including a choice between importing as a single entity or as components. From the top menu select Edit >> Preferences >> Import-Export >> STEP.
Converting STEP files to workable solids can be a bit complex, as you have discovered. It is best to use a very recent version, perferably a development version (0.20.xxxxx), since there has been quite a bit of new functionality added to the handling of STEP files.
Ultimately the problem remains that STEP files have no parametric history. Basically that means it is not possible to "change" something. It is possible to add, of course, but it is also possible to "defeature" the import to remove portions.
The FreeCAD forum is very active (I am a moderator), and any questions you have can be quickly answered by folks who work with STEP files.
The visibility of the Tree can be controlled by View >> Panels.
Gene