See the section "How Does AppVerifier Work?" in

http://msdn.microsoft.com/en-us/library/aa480483.aspx

This doesn't answer your question fully, as it fails to explain how
precisely they hook into the app.

ISTM that they use the HKLM\Software\Microsoft\Windows
NT\CurrentVersion\Image File Execution Options registry hook. For each
executable (such as python.exe), you can specify an alternative binary
that gets launched whenever somebody is asking to launch python.exe
(IIUC, by setting the "Debugger" value on the registry key). In case of
appverifier, they probably then load the original binary, do their entry
point rewriting, and start the binary.

There actually *is* a second question: what is it that AppVerifier
complains about? It may be useful to run Python in AppVerifier to detect
bugs - but any outcome of this is out of scope of this report, it seems.
If you are curious to look into this further, that would be much
appreciated.