Other than the per-user fonts, here are some other differences I found:
The "FontSubstitutes" key has some additional entries. The extra items are in non-english characters.
If you'd like to remove the extra entries, you may apply FontSub.reg. Note: It also resets your per-user Fonts registry key, which is empty by default. Create a Restore Point first if required.
In a default installation, the value "SQMEnabled" doesn't exist under this key.
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Mathematics\Standalone\4.0\
But it exists in your system. SQMEnabled is set to DWORD 0x0000001.
After reading this file "C:\Windows\assembly\GAC_MSIL\System.Windows.Forms\2.0.0.0__b77a5c561934e089\System.Windows.Forms.dll" Microsoft Math generates an error report (Windows Error Reporting).
The View Reliability History in the classic Control Panel should show more information about the WER report.
By the way, the per-user fonts can be removed via Windows RE.
Tracing "MaThType 6.9d" might be a good idea, when you're free.