That’s a valid point in principle. But in this case: yes, maybe?
We are comparing two optimized wheel-tire combos: the AR rims are optimized for 28 mm tires and hence, compared to the outer rim width, even 28 mm tires do not baloon out on them. (This is how I have understood the OP’s question: he wants to either get the regular 3.4s and use 25 mm tires or the ARs and stick 28s on them.)
The gains will probably be marginal (although I wouldn’t know how to quantify them). Moreover, the 3.4s are climbing wheels, so I don’t the OP is focussed on aerodynamics first (otherwise he or she would have opted for 4.5ARs or so instead). Nevertheless, you do bring up a valid point.