The actual repair would be quicker and easier from the top because you're not fighting gravity, but minimal finishing would be required doing it from the bottom - providing there is no liner involved.
While doing it from the top usually requires more finishing effort, it is pretty much the same no matter what the size. So I'd try to ascertain the extent of the rot. The larger the extent, the more likely I'd be inclined to do it from the top because doing the repair upside down can be a PITA if the area is substantial.
We re-cored a bunch of deck a few years back. Much easier from the top and the Fein tool was definitely the right choice. For core we used a pourable high density product fro NidaCore. It self leveled in the cut out areas. Also, it produced a fair amount of heat which helped it kick off even when it's cool. Be careful with the mix pot and pour immediately as the larger the amount of mixed NidaCore, the more heat it will make. We then used an angle sander to fair out the filled area and taper the glass on the edges, then two layers of glass and faired the surface w/ 3M, painted w/nonskid. Weight gain is really minimal in the big picture and you'll never have to worry about water in that area again.