As written, an armor's maximum Dex to AC will not affect Con to AC.
As intended? If it's not intended to work as written it would be a pretty glaring oversight from the designer. It's not like "dwarven fighter with heavy armor" is an exotic and unusual concept, and any experienced player is familiar with the concept of max Dex-to-AC when wearing armor.
Does it make sense? Why on earth would a restrictive armor keep the deepwarden from defending himself through sheer toughness?
(Or however you explain it?) He does loose the bonus if flat-footed, but that could be explained by assuming a voluntary component to the ability.
As for the OP, my first suggestion would be to let the ability stand as it is. A mid-level gestalt character with AC 26 is nothing special.
However, if you want to nerf the ability then restricting it by deepwarden level (option 1) would be consistent with similar PrC abilities.
As intended? If it's not intended to work as written it would be a pretty glaring oversight from the designer. It's not like "dwarven fighter with heavy armor" is an exotic and unusual concept, and any experienced player is familiar with the concept of max Dex-to-AC when wearing armor.
Does it make sense? Why on earth would a restrictive armor keep the deepwarden from defending himself through sheer toughness?

As for the OP, my first suggestion would be to let the ability stand as it is. A mid-level gestalt character with AC 26 is nothing special.
However, if you want to nerf the ability then restricting it by deepwarden level (option 1) would be consistent with similar PrC abilities.