Yes, thats how I manage my snapshot-/stop-mode backups and it works well. Just keep in mind that using multiple backup jobs to different namespaces will drop the dirty-bitmapping so backups will take longer. But on the other hand doing a stop-mode backup will drop the dirty-bitmap anyway.I would recommend that you use a datastore and work with namespaces there. Then you still have to add both namespaces in PVE (like @Dunuin said). On the PVE site you say that you want to keep all backups.
In the PBS you then set your prune jobs according to your requirements under Datastore -> "YOUR DATASTORE" -> "Prune & GC". Don't forget to take the namespaces into account in the prune job.