The documentation for waypoints is not matching the actual allowed API calls. It can be found at https://developer.here.com/documentation/routing/topics/resource-param-type-waypoint.html
Specifically, from this you should be able to use
geo!passThrough!y,x...
but it only allows
passThrough!y,x...
I have not tested, but this also implies using passThrough points will not work with the non geo waypoint types (links, streets).
Either fix the API or the docs.