Yes it did self level... and I've done this trick several times. Here is a gasket I made for a keel pin for the swing keel of a Balboa 26... In this picture you can see the cured product a little better.
Here is a pic of a gasket I made when bedding the pedestal mount for my tiller pilot.
To answer your question about the imprints seen on the ballast valve... I don't know what the PO did (I'm guessing nothing) so what you are seeing is the remnants of the old gasket. It appeared to me to be hard glue so I'm guessing that is the 5200 that had been used to glue the old neoprene gasket in place but... the gasket itself was long gone.
And if memory serves me right.. I put two tubes in to make the ballast tank gasket.
Hope this helps. BTW: The goop does stick well once cured. On my boat I waited about 36 hours and then gently closed the valve. The rubber becomes VERY hard in about 72 hours so I wanted mine to still be a little bit pliable so I could get a good tight seal. Now when I lower my valve I do see the imprints in the rubber so... I believe I have a very tight seal.