Yes and no

The panel that i think that you are talking about is the fuel tank inspection panel. If the only way to access the fuel tank is through the tray, then yes the factory will have an access panel there.

This is only found on utes that have a well body style tray. Aftermarket dropside style trays wont have this since you can get to the underside easy enough.

Aside from that, even if the tray does have an inspection panel, weather you can fit a battery in there is another question, and weather you think that putting a battery next to a fuel tank is a good idea is the questions that you have to ask.