Hi,
Unfortunately the ArcGIS for Server Maps for Mobile does not have any future at this point. I strongly recommend you to adopt ArcGIS Online or Portal for ArcGIS. These products provide you all the functionality you require.
If you want to support security on the ArcGIS Server Mobile Maps in a seamlessly manner you have to implement the coding. Fortunately, is not that much.
You can secure ArcGIS for Server using AD (as an example). This will secure both the traditional REST endpoints as the Mobile Maps. The difference between both is that the Mobile Maps use a cookie for persisting the security key and ArcGIS for Server uses a token on the URL.
You can request the ArcGIS for Server Mobile Server login endpoint using you AD account and get the token associated with your user. Then, you can use that token as a cookie in the next request (for getting the Mobile Maps content), and the request will be authorised.
They both use the same Identity store.
Cheers,
Jose