All new textures I am adding to the new PK3 file have a defined naming system.
Seems that names are limited to 8 characters, so I came up with a system where 4 letters describe the type of texture, two digits give it a serial number, one letter designates a subvariation of the texture and one character is saved for special cases. Except for the 8th character, all other characters are obligatory.
CITY02A is the 2nd city texture's first (basic) variation.
CHUR03D is the 3rd church texture's 4th variation.
For an example how this works: CITY13A is the basic wall texture using the big green stones. CITY13B is the same texture with a window on it. CITY13C is the same texture with a door on it. These correspond to the old ATOWN13, ATOWNW12 and ATOWND10 (or similar numbers, don't remember exactly) textures, but now they are clearly delineated as variations of the same texture and are shown together in DB2's texture browser.