Hey Chandler Callison,
In short, it'd be best to use the Route Layer directly from Navigator user interface or build your own Navigator link to bring the route into Navigator. The "Navigator Stop List" only includes the stop locations when bringing the route to Navigator. This means you lose the solved route (as well as a lot of other important details) and Navigator will have to re-solve client side with whatever transportation network is in the drivers current map.
With that said, the "Navigator Stop List" link is planned to be updated in next releases of Portal / Online to open the Route Layer itself in Navigator, but if you'd like to use links to open the routes in Navigator in the interim you can formulate your own in the format of https://navigator.arcgis.app?routeItemID=<itemID> (see more here Deploy—Navigator for ArcGIS | Documentation). This will load the route into Navigator bringing with it some extra important bits, such as travel mode settings, barriers, etc.
As far as solving routes client-side goes, the stop list will use the current maps transportation network (and travel modes) to solve a route to the stops listed. The Route Layer already contains the solved route so it only needs to be re-solved if the driver deviates from the current route. In this case the route will be resolved against the current maps transportation network using the analysis settings within the Route Layer (travel mode, stops / waypoints, restrictions, barriers, etc). If the transportation network is vastly different you'd likely want to publish your own MMPK with your transportation network.
Hope this helps, feel free to reach out with any other questions jwhitney@esri.com
Joel
