Basically you're letting the algae run out of nutrients as well as giving them no light to thrive. Its mostly the no light thing that gets rid of it, I found putting a handful of hermits in there as well got the job done as they had nothing else to eat but the algae.
Yeah it is a pain in the arse doing it for more than couple of months, I found that it depends on how much algae you have and the type of algae, browns seem to die off more quickly than say, green hair algae. For GHA it took a minimum of 6-8 weeks (this was on another batch of rock I "cooked" mostly I just didn't want to use it and was going to take it back to the store but never got around to it. It lived in a rubbermaid tote for about 8 months). At the time I cooked my rock I really really hated my tank and never spent more than a few minutes topping up the FW and feeding the fish. So really not looking so critically at the tank helped in my case
It certainly can't hurt just doing it short term although you won't see the full benefits. If nothing else it will at least leach out any gack into a different water source other than your tank. I doubt the algae will diminish much though, it can live for quite awhile without any light before it finally kicks off.