OK - I found out myself :) You need to pass ResourceSaver.FLAG_BUNDLE_RESOURCES flag :)
Entire code:
var scn = PackedScene.new()
scn.pack($Mesh24212)
ResourceSaver.save("/home/user/Downloads/mesh-comp.tscn", scn, ResourceSaver.FLAG_BUNDLE_RESOURCES)
But beware! There seems to be an error if you want to use the binary format .scn with compression - the texture is not persisted correctly :/