I haven't done this to a subie, but I did it to my old 1st Gen CR-V. Stock 95a alt, 1000w amp driving two subs, and a mid-range optima yellow top. Before the big 3 and optima, it'd go into protect regularly. Before big 3 with optima, still happened but a lot less frequent. Big 3 + optima, never happened again.
Definitely worth doing.