In the test I described below - I used Win10 Disk Managment to create & format NTFS partition, in a "new" offset from the disk start - in the free space appeared at the disk end after shrinking down the last partition. The result is not stable, but >50% tests without extra folders hack lead to inability to run UEFI boot of just installed windows. So this bug is reproducible with windows-based NTFS creation too.
I've created a new 30G partition and tried installing there a small win7 variant (1.5GB in esd file). I tested the old and new WinNTSetup version, each 10 times, in a semi random order, formatting partition before each test. The results are following:
5.3 Beta 6 - 3 successes, 7 failes
5.3 Beta 6.1 - 10 successes, 0 fails
So it seems to be fixed! However now it is also known that the behaviour without "extra folder fix" is not stable. Sometimes it boots fine. Note - the randomness is at install time, not boot time. Every installation either always boots or never boots. Maybe it is related to some random order of flushing cache to disk in the windows NTFS driver.