The problem is that you are trying to zip the geodatabase and add it with the add file option. You need to add the data in the geodatabase to a blank mxd and publish from there using the "share as a service" in the file dropdown. That is the process I use for anytime I am setting up collector and need to leverage the subtypes and domains. You need to make sure you are logged into AGOL in ArcMap. Chose "my hosted services" and it will be in your content on AGOL.
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