The implication of the question is that this extra 1000 miles should be added to Pluto's radius. The answer is no. For all of the solid planets, it's that solid surface (or solid+liquid surface in the case of the Earth) that counts, not the outer reaches of the atmosphere. The surface is a clear-cut, non-arbitrary boundary. The atmosphere? They can extend a long way out. A non-arbitrary boundary is always going to be preferred over an arbitrary one.
That's not possible in the case of the Sun and the giant planets. A somewhat arbitrary boundary is needed for those bodies. That somewhat arbitrary boundary explicitly excludes the upper reaches of the atmosphere, which extends out for many thousands of kilometers. For the giant planets, some use a tenth of the Earth's atmosphere as defining the arbitrary "surface", others, one atmosphere, yet others, ten atmospheres. That factor of 100 variance in pressure amounts to about a hundred kilometers. That's not that much considering how big the gas giants are.