You don't need to clear them out going to forward to another 2 nodes will reset the previous nodes.. the way I do it is to use the ABC or 123 way points between the 3 locations and cycle them in a circle so that I know they get the respawn.. just check each mode gather what you need an move to the next and they'll refresh.

I believe normal nodes when something is hidden like seeds only yield a single gather and the timed nodes will yield multiple due to the methods of respawning.. I could be wrong tho.

No macros that I know of.. you could always use thr confirm button on keyboard if your playing on PC otherwise no it's just target and go.

Good luck.. gardening is very time consuming and frustrating.. world of advice if an update or downtime is scheduled make sure you store the garden without gathering.. it will pause the rotting timer