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SEAL members (and other SF troops) do pretty much choose their weapons of choice, within the limits of weapons used by the military. An M16/203 is a good combo, depending on the enemy you may be facing. The M16 gives a longer range than the M4 or other short-barreled weapons, adn teh M203 gives some area supression capability.
Actually, we have the option of purchasing gas piston uppers such as the HK 416, which is outside the purview of regular military stocks.
That said, I spent a few weeks out at Coronado Island in November, so take this for what it's worth:
Those members of the Spec Op community you refer to no longer use the A2. They, as we, have the Mk12 SPR for longer ranges. In fact, last month we received our .300 Win. Mags (Mk13) which they use as well, hence the "Mk" designation.
There does seem to be a misconception about shorter range on the M4. The shorter barrel results in lowered muzzle velocity, but effectively the range is the same. The biggest difference between performance of the M16 and M4 is the sight radius, which is obviously shorter in the m4. The correct utilization of available optics minimizes those differences.