The new paradigm in 3e quickly became different than that in the older days. In 1e/2e, anything outside the core book was understood to be purely at the DM's discretion, and the ruleset in general as well. In 3e, though initially things like prestige classes gave lip service to that.
I don't disagree that things changed (although I think it happened much later than you claim). I do disagree about paying lip service in 3.0. Between the PHB and DMG, there are several passages stating that the DM is in control of how the game is run, can make changes and even the presentation of many variant options for tailoring the game.
PHB:
P. 4 Rule 0
p. 18 Customizing Characters
p. 60 Sidebar: Access to Skills
DMG
P.6
"Let's start with the biggest secret of all: the key to Dungeon Mastering (Don't tell anyone, okay?). The secret is that you are in charge. That is not telling-everyone what to do sort of in charge. Rather, you decide how the group is going to play the game and "you decide how the rules work, which rules to use and how strictily to adhere to them."(DMG p.6).
"the whole tenor of the game is in your hands".
P.9 "Good players will alway recognize that you have ultimate authority over the game mechanics, even superceding somethng in a rule book"
p.11.
"Every rule in the Player's Handbook was written for a reason. That doesn't mean you can't change them for your own game"
"As DM, you get to make up your own spells, magic items, races, and monsters!".
P.25-26 Modifying Classes
- Modifing Character Classes
- Spell Lists for Variant Spellcasters
P.27 Prestige Classes
"Allowing PCs acces to prestige classes is purely optional and always under the purview of the DM"
" Prestige classes are idiosyncratic to each campaign, and DMs may choose to not allow them or use them only for NPCs"
P40-42 Variant 1st Level Multiclass Characters
P41 Advancing Levels
- Access and Training
- Variant Learning Skills and Feats
- Variant Learning New Spells
- Researcing Original Spells
- Variant Gaining Class Abilities
- Variant General Downtime
- Variant Gaining Fixed Hit Points
p.66 Combat: Damage
- variant Clobbered
- variant Death from Massive Damage Based on Size
- variant Damage to Specific Areas