The Battle of the Atlantic is the name given a series of engagements that occurred between 1939 and 1945 - how is that connected to a one-day long invasion? The difference in terms of time span cannot be ignored.
Can we please remain on topic? 
Your argument is that troop transports in FreeSpace are too vulnerable to flanking attack during a landing.
I'm telling you that the situations are totally analogous. Convoy your transports, defend them, perform the landing. It's exactly like anti-submarine or anti-cruise-missile work in near-modern NATO/USSR wargames. Or, as I pointed out, the Battle of the Atlantic, defending a single convoy against sub attack.
Believe me, in Harpoon I've performed amphibious assaults as the Soviets on Keflavik, and defended against them as NATO, using air, surface and sub assets. It is not significantly different from what FreeSpace has to offer, and in fact FreeSpace transports are arguably in
less danger even with subspace.