First, are the tanks inside or outside a building? From the description, it appears the tanks are located outside of a building.
The standard that governs the installation of stationary combustion engines is NFPA 37. If the tanks are installed in accordance with NFPA 37 and are located outdoors, section 6.3.3 (2002 edition) requires spacing in accordance with NFPA 30. NFPA 37 does not contemplate a condition such as explained. If the tanks are located inside a building, tank shell-to-shell separation distances do not apply. See NFPA 37, section 6.3.2.
If the aboveground storage tanks are outdoors I would suggest an equivalency using section 1.4 of NFPA 37. You may be able to demonstrate that your design offers additional safeguards or safety features that can be used to eliminate the separation distance requirement in NFPA 30, sec. 4.3.2.2.1. One equivalency is to provide overfill protection on the tank fill connection, which limits the potential for a fire resulting from an overfill. Spill containment basins at the tank fill connection could also be considered so in the event of an overfill, the spill is contained. Be careful on this because I have seen overfilled tanks discharge product through the tank emergency vent. Another concept for equivalency (although not popular) is to provide a water mist or dry chemical fire suppression system in the enclosure. This could be shown as equivalency to the < 3 ft. shell-to-shell clearance. Any equivalency requires the approval of the authority having jurisdiction.
I've reviewed plans and inspected multiple generator sub base tanks but have never seen two generators in one enclosure. Does the owner realize that putting two generators in one enclosure would likely mandate lock-out/tag-out protect the generator technician, which then negates any standby / emergency power? A little more detail please.