which sealant can be painted over?

Most sealants except silicon can be painted. The information is usually on the tube or the data sheet. My choice for that job would be a polysulphide such as Boatlife or Arbromast which will enable you to remove the hatch if necessary.
 
Fairly certain CT1 can be painted over fine. Someone might want to verify that.

I painted over some CT1 in the spring of last year and it hasn't lifted off or cracked.

But it was ordinary marine enamel not 2-pack.

The manufacturers have a help line which I found 'helpful'
 
Just make sure you can remove the panel (without structural damage) when you need to - CT1 is an adhesive.

And - just because you've installed a new engine doesn't necessarily mean you won't have to remove it again - ask me how I know :p

I used Arbomast BR for mine - but I have a cockpit floor boards on top which protect the exposed sealant.
 

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