Hi Fred,
The answer to your question depends on the mobile device operating system that you are using running Collector connected to the R2.
Android OS: Collector is able to read the TMM custom real time and position output configuration. With this workflow, you would connect in TMM, make your configuration, then disconnect from the R2. When Collector connects to the R2, it will be able to read the configuration file stored by TMM and utilizes the custom configuration including orthometric heights.
iOS: Collector on iOS is different because of its integrated configuration of the receiver as you mentioned. Communication from within the Collector app through the implemented TPSDK does reset the receiver and is not currently able to support the custom position output configured in TMM (so it cannot support orthometric heights at this time).
Trimble is working closely with ESRI to implement support for the custom position output configurations TMM allows in the recently announced Field Maps application. If this workflow is of interest to you on iOS, then I would suggest getting involved in the Field Maps Beta program with ESRI so you can be among the first to use the beta version that includes the Trimble receiver supported workflows. We are expecting that to be out soon.
- Lane Carter
Trimble Geospatial Support