Another way to see this is to look at:
Reduce[Exists[{x, y}, x > 1 && y > 1 && x > Sqrt[x + y]], {x, y}]
(* ==> True *)
Reduce performs quantifier elimination so you will in general end up with an expression involving only free variables (of course only in those cases for which quantifier elimination can be done, i.e. basically polynomial formulas with real coefficients) When there are no free variables, the expression will be either True or False. Now when you use FindInstance in this case you are in effect asking for an instance of True (in terms of x and y) so any pair of numbers will be an answer. In general,
FindInstance[expr, vars, domain]
is logically equivalent to
FindInstance[Reduce[expr, vars, domain], vars, domain]
although you will not usually get the same answer if you evaluate both (of course this is a very inefficient way to go about finding instances...)
Looked at in this way, I think it becomes pretty clear that way that there is no point looking for instances of bound variables since they will be eliminated from the expression before FindInstance starts looking for "instances".