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The statement that the Argo has two Fighter Cubicles, in reference to four Mech Bays, seems to indicate that the Argo has space aboard for two ready to launch Fighters of any type, and the massive cargo capacity would enable anyone using the Argo to carry more than enough spares to keep them operational, as well as space to keep replacement Fighters of any type as well. Given the operational needs of the Argo's primary mission statement, I would assume (yes, I know about THAT word!) that the Argo carries two ready Fighters and up to four replacements. This would not excessively strain the overall cargo capacity of the Argo, nor cut into the total cargo tonnage by a significant amount.
Given that the Argo was meant to be an armed and armored mobile space station, servicing other Drop Ships while performing Solar System Surveys of a new planetary system, it is not inconceivable that the twin bays might be 'hot loaded' during such a mission. Hot Loading being a term for launching the first pair, readying and launching the four additional Fighters, and only retrieving them as then need refueling and servicing. If the bays were currently occupied, Fighters could use the Multi-Docking Ports to await their turn at servicing without undue fuel expenditure.
Assuming a full fleet for such a Survey Mission, it is also possible that there would be Leopard Class Drop Ships converted to CVS (Carrier) design, where the Mech Bays are converted to more Fighter Bays. A couple of the CVS Leopards, along with a combat Union Class, a couple of Freighter Unions, Three or four 'standard' Leopards, and a couple of Jump Ships, would make a Deep Recon Survey Mission both possible and protected against unexpected events such as Pirate raids or any other conceivable threat. The Argo's built in HyperPulse Generator system enables communications over vast distances, and thus the Argo could 'whistle up' a Battle Fleet if needed for protection... At least as envisioned when the Argo and her sister ship were designed, laid down, and the Argo itself being eventually deployed.
I admit I may be wrong about all this, but my above statements seem logical and 'sane'. Feel free to refute me at your leisure.