A general discussion on the size of the Sovereign
Ex-Astris Scientia has a good article on the Nemesis
The model doesn't actually feature any new decks and the pylon changes weren't actually given an in-universe explanation.
And the Enterprise
as of the end of Peaceable Kingdoms
doesn't have Slipstream capability, yet, but might for the upgrades mentioned before her next mission. Also, nacelles don't really impact slipstream.