Garmin Connect's web importer ignores waypoints. It only reads route/track data to build a course, so your stops get dropped there — regardless of the file. Use one of these instead:

• Copy to the device over USB — put the "stops only" file in Garmin/NewFiles/ (some models use Garmin/GPX/). The device imports it on next start and the stops show as saved locations.
• Garmin POI Loader (desktop app) — converts the file into custom POIs with proximity alerts as you ride past. Best experience if you want to be warned "water in 500 m".
• Komoot / RideWithGPS — both read GPX waypoints properly and sync to your device.

Wahoo and Hammerhead read waypoints from a combined file without this issue.