I'm not real familiar with the deck plan or any model changes. Looking at the new Odyssey on the Hobie site though, it looks like there is a 6" hatch at the forward bulkhead and an 8" hatch in the rear cockpit (somewhat similar to our tandem Oasis)
I believe your forward bulkhead is too narrow for an 8" hatch, but the rear cockpit area might accommodate the 8". Including the flange, it has an 11" diameter, so you might make a template of 11 1/4" and see if you have the flat surface to support it.
The dent between your scupper holes was likely caused by the scupper cart. Normally this pops out in the sun, but an extended time on the cart might cause this to become permanent. If you get access (new hatch ?), you might try
lightly wedging a piece of wood in there for a day or two in the sun and see if it pops out. Or you can just leave it alone -- it shouldn't hurt anything.