I use Picker Extended and Rail tools for some QoL enhancements such as marking empty miners and auto placing rail signals.

The drones currently do not fulfill those orders, when I re-mark the miners manually the drones react correctly.

I suppose the mod that does the deconstructing is not raising the appropriate events, which means there is no way my mod can know

So I looked into it and when the deconstruction is called without a player (/c game.print(game.players[1].selected.order_deconstruction(game.players[1].force))) (should trigger on_marked_for_deconstruction) then the construction drones will not react. When the player is added to the call the drones will react.
The construction doesn't work if there is a blueprint built via script (e.g. /c game.print(game.players[1].cursor_stack.build_blueprint{surface=game.players[1].surface, force=game.players[1].force, position={x=0,y=0}, by_player=game.players[1]}) or there is a ghost placed via a script (/c game.players[1].surface.create_entity{name="entity-ghost", position={x=0,y=0}, force=game.players[1].force, inner_name="transport-belt"})) (should both trigger on on_built_entity right?).
As far as I see these script calls should trigger the drones to (de-)construct, am I correct in the assumption that I would have to report this to the forum as these calls not triggering event seems to be a base game matter.

The mod has to specify whether to raise the events when creating entities.

The other is a limitation, the API event for on_marked_for_deconstruction doesn't include the force which ordered the deconstruction, so I can't do anything with the information