If you're having trouble with MSI, use MSI logging (and specifically - create the log as part of the default run). Treat it as a "regular" software distribution install - with all of the gotchas & troubleshooting approaches.
MSI's should work just as well as anything else - "timeout" is a bit odd, but may make sense once you enable MSI logging to see what the MSI is either waiting on or doing or whatever?
I think the timeout was caused by an incorrect ARGS statement that I used on my initial Patch Install Command. I already found the correct ARGS statement that I need and the Deployment Task that I created went smoothly.
The ARGS statement that am using now which actually works / solved my problem is
ARGS /i "$(FULLPATHTOBINARY)$(PATCHBINARY)" /quiet /norestart