However, if my scenery.cfg is corrupted, how is it that (a)I do not get a scenery error flag when FSX loads, and(b) how come I can select any or all the airports including all my non-FSDT add-ons without any problems?
There might be two possible explanations for this:
1) FSX doesn't use the standard Windows routine to read .INI files, but has its own parsing routine, which has been made more robust against syntax errors, so it's able to just skip the problematic area, instead of refusing the read the file or, probably, the sections after the corrupted one.
Both GSX and (likely) Flightsim commander, use standard (provided either by Windows or by some standard library) .INI parsing routines, that are more formally correct, so they treat as errors what FSX is able to accept.
2) BECAUSE of FSX is running in Compatibility mode, it's reading from another scenery.cfg file, instead of the one running under C:\ProgramData\Microsoft\FSX
Again, not possible to know without having a look at your scenery.cfg and checking if it's really corrupted.