Based on context ("By baking inspiration into the core... we have the structure for more in-depth rules modules"), I think it's pretty clear that Mearls is talking about the former. That's what "baked in" means; a "baked in" mechanic is one that is tightly integrated with the ruleset and can't easily be removed. There will be more complex optional systems around inspiration, but inspiration itself will not be optional.
Then it comes down to what does "easily removed" mean. For instance... the d20 is a TRUE "baked in" mechanic. The entire game is built around using that die to generate the random numbers of a certain span in a certain percentage of occurence needed for the game to work. Using something other than a d20 (like 2d10 or 3d6) would affect so many other systems in the game that making that change would be (at least in my opinion) extremely difficult and time consuming.
But is "equipment" baked into the system? Could you remove weapons (for example) from the game entirely and still play it? Sure... you just use nothing but spellcasting classes and adjust the monsters you encounter to fit that paradigm. But there's no real issue across most of the other systems in the game if you don't use weapons, because there is an easy work-around-- don't use any classes or monsters that use weapons. So are weapons "baked into" the system? Would we consider weapons to be a "core part of the game"? Most of us probably would... even though it wouldn't be that hard to work around them if the table chose to go in that direction.
So that's what I'm getting at. How baked in is "baked in"? I mean... as Klaus just mentioned, if the Inspiration rule is based upon how often the DM gives the award and the choice of "Never" is an option... is Inspiration really "baked in"?