Doh! I should have spotted that one, having spent some amount of time looking around in there for something just like that :-)
Probably too late now and too difficult to implement, but I wonder if there might be a gentle way to indicate where progress still needs to be made? eg Different color batteries depending on environment, and color-coding the battery gathering point accordingly, so you can think a-ha there's a blue slot still open, I probably need to be re-exploring the water areas. A little like the function served by the obelisks in the Witness.
Anyhow, happy I've now escaped, and I found the ending delightful. V inventive use of the message system!