This problem is most pronounced for non-application file searches, as that is where the great majority of my searches are directed. I am not noticing missing applications this time and yes, application searches were also causing problems on that original post, but problems were not limited to those types.
As stated in the OP, this problem manifested on a virgin system install, so nothing else had been installed (nor has anything related been to-date on this system).
I don't tend to search for system apps, so I don't have a lot of examples but winver.exe does return in a Start11 search. However, here's a search for ubiquitous functionality that works as expected in native search but fails in Start11:
Search for ClearType
Windows returns...
Start11 returns...
This example may demonstrate that the differences are wide ranging, but the most painful difference is in Start11's ability to locate documents and files that readily appear in Windows start search. Even files that are present in app jumplists in Start11 are not returned in a Start11 search.
Until yesterday, I was running the latest release version of Start11. Just to make sure nothing would be different before posting, I installed the latest Beta 1.22 version.