Strategic Reserves are separate from other Reserves units (deep strike, aircraft, etc) and the limit only applies to units set up with that specific method.
The bigger problem with the Manta is that it can not arrive wholly within 6" of a table edge and therefore can not shoot on the turn it arrives. And most of the time your opponent will simply block its movement on the following turn, forcing it to fly right off the table without ever doing anything. It's a meme unit that is not meant to be played with in real games.
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