...I think the risk that microsoft starts blocking installs for no apparent reason is very unlikely.
.msi files are standalone installers which do not need network access so I cannot see how Microsoft could block them even if it wanted to.
Windows Installer is as far as I know a framework that is part of the windows installation and as such microsoft can change functionality of the framework as they please, including verification against unwanted software. Theoretically this could come with any windows update. Right now there is no online verification of msi-files, but the possibility is there.
That is different with stand-alone installers, which Windows Installer is not. At the same time 3rd party solution would be very likely in such a case, which makes it even less likely.
