Hi,
I ran into something similar, so here is what I found. Your log already gives the main clue: Error 27592 says the installer needs .NET Core Windows Runtime and ASP.NET Core Runtime for the selected blades. This is not the classic .NET Framework requirement we have had for years, it is the newer .NET runtime.
The reason it works differently when you run it by hand is the installation wizard. When you launch the package manually, the wizard detects the missing prerequisite and offers to install it (that is the "Install Prerequisites" screen you saw). A silent MSI install through SCCM does not go through the wizard, so it stops with the error instead.
Check Point describes the same behavior for .NET Framework in sk182480: with the wizard, the .NET installation and reboot are handled for you; without the wizard, the install exits with an error and has to be run again. The same sk also mentions that if the exported package does not include the .NET installer, the installation fails.
What I would try with SCCM:
- Package the .NET Desktop Runtime and the ASP.NET Core Runtime as separate SCCM applications and add them as dependencies of the Harmony Endpoint application, so they are installed before the MSI runs.
- Test on a pilot machine first to confirm which runtime version E89.26 expects. I could not find the exact version documented yet, so it is worth confirming with TAC or checking the install log after installing the runtime.
- When you export the package, leave "Minimize package size" unchecked so the dependencies are bundled as much as possible.

If anyone from Check Point can confirm the exact runtime version required from E89.26 onwards, that would help a lot of people planning the upgrade from E88.x.
Hope this helps!