Topping off in the fermentor after a partial volume boil is a common practice.
You would add 2.5 gallons of clean water to the fermentor if your boil volume was 2.5 gallons and the recipe is for a 5 gallons.
The 2.5 gallons top off water would be added to the fermentor first. This prevents damaging/stressing a glass carboy. The cooled wort would then be added plus a bit more to adjust for boil off is necessary.
The cold top off water helps cool the wort to pitching temperature.
I think what he's asking about is adding water to secondary, not adding water to primary (which of course doesn't matter in primary other than hop utilization will be less with less wort, because other than that it makes nodifference if the water is added before the boil or after to the concentrated wort).
But going into secondary, you shouldn't have to dilute it much more. If it was 5 gallons after you added water in the primary fermenter, then you shouldn't have lost much when you took it off the trub and put it to secondary, unless you dry hopped with leaf hops or a ton of pellets in primary, and sucked up too much of your beer).
But a little bit of water isn't going to dilute your beer's taste in any significant way
Also, if you're dryhopping or adding anything else in secondary, then you may not have to add much water at all, but it's good practice to not have too much headspace (I've read 2 inches). My understanding is that in secondary the yeast is finishing up and not producing much CO2, so your risk of oxidation is greater if you leave too much room for it.
Maybe those who know more can say how much of a risk it is to have extra headspace, but a small amount of dilution shouldn't be a concern.
