I’ll venture an admittedly pure WAG:
Is it possible that the ‘output side’ of the controller is simply a on-off type switch??...If so then,
a) Neg Array to Pos controller output side, thru controller, Neg controller output side to batt Neg post.
b) Pos Array to Pos controller input = equalizes within panels depletion zone (Pos) diodes - (no adverse effects).
c) Pos batt to controller Neg input, passing through inductive coupling (??), then completing a path to the array Pos - no conflicts with above item ‘b’...
But to make this madness all possible, how does the coupling become inductive??...Possibly a consequence of the controllers on-off pulsing action...
As I said, this is just a wild arse guess - lol
3 tons, after a shot of Jack