speakeasy
yep.. you have it figured out
and as you have found out
some shortcuts cause problems, down the road
you need to rewire
or disconnect the solar panels from the controller and take the batteries inside for storage
there are good reasons for wiring the controller directly to the batteries
be mindful that most controllers must be connected to the batteries before connecting the panels
and the panels need to be disconnected from the controller before disconnecting the batteries from the controller
otherwise the controller will be damaged
my best guess, for your controller still working is because the TT wiring devices, presented a load, to use the current/amps from the controller
normally voltage spikes would kill the controller, disconnecting the batteries while the panels are connected and supplying power