104 degrees is far from boiling. I have personally have had that temperature and more several times. (Last time it was Palytoxin poisoning). But of course i do not put the warm stones directly in a "live" tank.
That risk would only be theoretical. I do not see any risk for such a fast bacterial build up.
And the stones in the warm tank will not have a fancy bacteria build up. They are just lying there a day to get warmth from the outside.
I have used the method several times to get rid of Aiptasia...
I know it is a long time. A very long time.
I would just put the stone in a separate tank and heat it to more than 104 degrees for 24 hours.
Of course the most in and on the stone will die so the stone has to be cured with start up bacteria in another tank preferably with circulation and...