The installer is writing mostly to these keys:
HKLM\Software\IvoSoft
HKLM\Software\Microsoft\Windows\CurrentVersion\Explorer
HKLM\Software\Microsoft\Windows\CurrentVersion\Policies
HKLM\Software\Microsoft\Windows\CurrentVersion\Run
HKCR\CLSID
HKCR\AppID
Anything else is done by Windows Installer itself, or some unrelated software.
BTW, Windows Installer creates a checkpoint before installing the software. Maybe that's what you are seeing. You can disable it by adding MSIFASTINSTALL=1 to the command line of the installer EXE:
https://msdn.microsoft.com/en-us/library/dd408005(v=vs.85).aspxIf that's not it, and you are still interested to figuring it out, I would run a tool like Process Monitor to see what exact registry keys are written to and by which process.