I expect it would for two reasons. First, the Gore Tex Pro shell is a three-layer laminate, so even if it breathes some it'll never flow as much air is an unlamented material would, and second, with the liners out the Neptune will be looser (since it's cut to fit over two layers).
Talking about the fit, the Cycle Gear near me has the Neptunes (And Sand 2 and a few others) in stock, so I was able to try them on. The right size for me in the Neptune would be XL, but the Poseidon (with one less internal layer) fits me perfectly in a Large.