I Need Ideas From You Creative Types!

If you run your cable lock through the handles just remember all it will take is a saw of almost any kind to cut through the plastic handles and walk off with them.

B.O.

A metal shop would make quick work of it if you provide accurate dimensions and specs, such as cooling vents, and rolled edge, or gasketed edge to keep from dammaging it and tray. Basically a box with holes or slots for power cables and slots/vents for cooling, maybe even a small fan and cable, to run from generator, on inside, of box on vents. I one piece rolled over, flat top ,for two sides and top, and side pieces welded in or rolled in. Punched vents, on side with upper edges rolled out so rain won't run in or at least as much.
Since punching is slots etc is expensive just punch round holes.
Stainless screen careful not to crease spot welded inside or just glued, and fewer bug problems
Could even put latches with locks on bottom to match tray perhaps. One hundred in stainless 10 gauge .12 gauge sheet, plus two hundred perhpas for work. Maybe even cheaper if they have some odd pieces around. Understand I don't know the cost just estimating, based on a local machine shop that use to be not too far away 20 years ago.
If you are going to design something do it right. You can really guild the lilly if you got the money.

1/4" plywood with some stock in the four corners would do the trick. For a nice finished appearance, aluminum angles at the corners and aluminum C channels over the top edges would dress it up somewhat. Avoid making it too tight. I'm not sure how much stealth you can really gain since you'll be having the top open...maybe a dark colored window screen would help hide the view somewhat while still allowing plentiful air circulation.

I'd say simple plywood ends would suffice as you describe. Or...build a framework of pvc and cut a tarp to fit around it.

I think you'll end up moving them off the platform for operation so a plastic bin will be indiscrete for transport.

If you're adamant about not moving them off the carrier and have some $$ to throw at it, a custom enclosure with soundproofing, vibration isolation, and active air flow has been done. It's a rather complex enclosure so too much to describe. Search for "generator enclosure Honda" and you should find the good ones.