mx5cartalk.com

Should there be a rectangular seal which fits the drain opening in the bottom of the tray to provide a seal between the tray and the rectangular drain tube below?

Drain tube?
That is actually an air pickup tube to provide some cooling from the front of the car.
They do have foam around the connection points which deteriorates. Not really important. The foam realistically was likely there for reducing noise due to the plastic parts rattling against each other then acting as a seal. If it bothers you just put some tape or similar around it.
If you look closely you will also have a second vent that directs the air out of the battery box towards the alternator.

When a battery leaks in a NC it juts makes a big mess anyway all under the tray onto the steel rail as the tray has multiple hols in it.

See this link.
Sort of talks about it all.
https://forum.miata.net/vb/showthread.php?t=666011

Thanks Luke including the link. I realize now its an air pick-up tube. The foam seal had disappeared (not a great design) so I replaced it with another I cut from a piece of felt and used auto gasket sealant and tape to secure it and the tube in position. Perhaps not really important as you say but tidies things up. Removing the battery tray revealed the white powdery stuff had formed where you said it can so I cleaned it up. Wouldn't have seen it otherwise.