Hi Line,
Your requirements:
"There are 2 goals we hope to achieve with our implementation of Portal:
1) Give Portal users the possibility to create new Feature Layers from Portal. From what we understand this can only be achieved if we use ArcGIS Data Store; using an Enterprise geodatabase as our Data store does not unlock this options.
2) We would like to be able to update features located in our Geotatabase using Feature Services for use in Collector. When Data Store (software) is installed all Feature Services are published as Hosted Feature Layers. When the feature layer is hosted in the Data store edits are no longer synched with our ArcGIS Server Geodatabase…"
Based on the above, for item 1, I would use the ArcGIS Data Store. Yes, you could use an enterprise geodatabase, but internal testing has shown that the ArcGIS Data Store performs better and is able to host more feature services for Portal for ArcGIS. Also, as Jacob said: if you want to enable and publish scene services (3D data) then you must use the ArcGIS Data Store because scene services are not supported by enterprise geodatabases.
On item 2, I would use an enterprise geodatabase as a managed data store (i.e., data storage option) for the feature services that you publish to your ArcGIS Server site. These services could be used to support your Collector for ArcGIS editing workflows.
The point being, I would actually have 2 separate "data storage tier" options:
1. ArcGIS Data Store for your hosted feature services
2. Enterprise geodatabase for your ArcGIS Server site feature services
Hope this helps,