Dow 795, GE SG-4000, or Sika Flex 295 UV with primer are the best choices.
The details are here: Which Sealants To Use
Select Plastics is the largest marine hatch repair facility in the world.
Lexan is not the best choice for a hatch unless it was lexan originally. Only Bomar hatches with the metal cross beams use lexan. Every other hatch manufacturer - Lewmar, Bomar, etc all use cast acrylic for the very reason you found. Lexan deflects when stepped on and the seal will break - regardless of sealant type. Cast acrylic is also much more scratch resistant and will last years without crazing, lexan crazes in a few years.
If you have not yet purchased the lexan use cast acrylic (plexiglass) instead for the reasons above. Lots of good information at the link posted.