Welcome to the dark side.
As for Windows package managers, I can fully support the statements of Michael and Andrew: MSI is the worst, and Chocolatey is so good that Microsoft picked it up.
(Both need administrator rights, so for myself: not applicable.)
Maybe talk to Carsten Winkler at HZB/BESSY (author of LabCA): he is knowledgeable with both technologies, as far as I know.
If you think about a broader approach for developing and deploying EPICS based systems within the Fairmat initiative, I would do a one size larger round by doing a proper design: collect requirements (with the choices in mind that the read-me points out), have partners sign-off on those, do a design and convince them with a prototype. If you want to establish a standard, you need to involve your clients early on.
For deployment of Windows IOCs in a larger facility, Mark Rivers and Freddie Akeroyd would definitely be people to talk to. Beamlines are prototypes for platform diversity (isolation and robustness); ISIS migrated their Instrument controls to EPICS@Windows (scalability and consistency).
Cheers,
~Ralph