RTC, Sounds like we are using the same basic approach. I haven't explored subtypes yet. Ben in his comment mentioned using the domain sorting tool, and I highly recommend using it. I had been looking for the easiest spot to fix the sorting in regards to adding new features. It seems to me that using the REST API is the best place to do it. Your link to jsfiddle looks like an interesting tool to help sort the Types section of the JSON file. And before making updates, I recommend jsonlint.com for JSON validation.
When I used the Manage New Features in ArcGIS Online, I found that the contentType in the drawingInfo section was being changed from image/png to null. When contentType gets set to null, the layer is no longer downloadable in Collector for off-line use. The layer will still work in Collector for on-line use. ESRI support is aware of this issue; their response: " This anomaly can be classified as an ArcGIS Online where the AGOL changes the "contentType" in the symbology description to <null>. Essentially, this leads to the symbology contentType defined as null in the offline geodatabase and as such the Collector for ArcGIS fails to read and assimilate the features."
For fixing the feature template order, I would recommend using the REST API and just updating the Types section only. Using the whole JSON file, particularly the DrawingInfo section, has, in my experience, causes the contentType null problem, which you would want to avoid. Experimenting with a copy of your layer and making backups is also recommended.
RTC and Ben, I appreciated receiving your comments. Thank you.