One thing on the seal you might consider unless you have a new deeper tray for the taller modern batteries is maybe glue a thin piece of sheet rubber on the bottom of the cover. That might provide a bit of a dust and air seal as well as some electrical insulation in case the battery might get jarred and somehow a cable connection winds up a bit too close to the cover.
One possibility on the cutoff switch if there is no clear and convenient spot is to locate it in a more appropriate spot and then actuate it from a distance with a rod or push-pull cable. Jegs and Summit have commercial versions of remote actuation means or if those wouldn't work for whatever reason you could make your own. I built custom versions to provide a rod extension to a switch mounted on the firewall for one car and a push-pull cable to operate the switch under the battery tray on another. That was done to have the operating knob within easy under dash reach. I also placed the switch in the ground cables.
First pair of photos are the rod extension and second set are the of the push-pull cable. All parts needed for both methods came from McMaster-Carr.
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