hello and welcome here,
actually there is no api, the synfig plugins work directly on the project (xml) file. Save a project in .sif (no compressed file format) and take a look inside it.
So yes, you can remove all waypoint from a plugins. But has there is no API you can’t really interactively choose what the plugin will change.
I think of two way to bypass this problem,
- adding an user interface in the plugins displaying the waypoints
- using the layer name, to pass info to your plugins
But this is not a very easy way for all the things your are talking about.
Also, this thread can interest you : Waypoints … what could be the future of…?