We already know that clean installs have Store applications working. My reason for not doing a clean install is that I want to keep my non-Store applications working as they are, with settings that have been working and continue to work.
Yes this PC and its latest BIOS and drivers are old. They're old when clean installs are working. They're old on 3 other PCs of the same model where upgraded installs continue to work.
Yes, KB4505903 was installed again after the in-place upgrade. It also had been installed before being removed by the in-place upgrade, though it had not been easy to get it installed due to repeated failures. After the in-place upgrade, KB4505903 installs immediately.
I do not see anything in Malware Bytes settings that could prevent Store applications from installing. Also Malware Bytes doesn't prevent non-Store applications from installing, though I don't have a problem with non-Store applications anyway. Windows itself has an option which I have not set and Windows itself also doesn't prevent non-Store applications from installing.
A few years ago I used GPEdit to make Windows Update notify me before downloading and installing updates, the same as used to be available as an option in Windows 7 and XP, so that I can be aware and save my work before rebooting. I manually let Windows Update install all updates.
I have not tried CCleaner.
Yes, Reliability History shows that the following Windows Updates failed. There are duplicates in the list. The number of failing applicatinos is likely greater than this.
9NBLGGH4LS1F-Microsoft.StorePurchaseApp
9PK21VDD7LD9-Microsoft.NET.Native.Framework.2.1
9MZ8BK1XV75W-Microsoft.NET.Native.Runtime.2.1
9NBLGGH4LS1F-Microsoft.StorePurchaseApp
9PK21VDD7LD9-Microsoft.NET.Native.Framework.2.1
9MZ8BK1XV75W-Microsoft.NET.Native.Runtime.2.1
9WZDNCRD1HKW-Microsoft.XboxIdentityProvider
9WZDNCRFJBMP-MICROSOFT.WINDOWSSTORE
9PK21VDD7LD9-Microsoft.NET.Native.Framework.2.1
9MZ8BK1XV75W-Microsoft.NET.Native.Runtime.2.1
9WZDNCRFJBMP-MICROSOFT.WINDOWSSTORE
9PK21VDD7LD9-Microsoft.NET.Native.Framework.2.1
9MZ8BK1XV75W-Microsoft.NET.Native.Runtime.2.1
9WZDNCRFJ3PR-MICROSOFT.WINDOWSALARMS
9NBNPFNSWTGB-Microsoft.UI.Xaml.2.1
9WZDNCRFJ3P2-MICROSOFT.ZUNEVIDEO
9WZDNCRFHVN5-MICROSOFT.WINDOWSCALCULATOR
9NBNPFNSWTGB-Microsoft.UI.Xaml.2.1
To repeat, you do not need to tell me that a clean install might work; I already know that it does. The question is whether Microsoft can fix an existing install that Microsoft screwed up. The existence of tools like sfc and dism suggests that Microsoft intended to let some kinds of breakage be repaired.