On ClickPad/TouchPad, they were stored in the Boot1.
I haven't investigated this on CX/CM yet.
As far as I can tell from various experimentations, it seems that the Boot1, which is common to CX and CM models, knows about both CX and CM keys, but adds a model check for running the Boot2 and Diags.
But the Boot2 only knows about the model specific keys.
That's why for example you cannot directly run a CM Boot2/Diags on your TI-Nspire CX.
But if you flash the TI-Nspire CM manuf splashscreen (which have no header with the model ID unlike the Boot2/Diags) on a TI-Nspire CX, the Boot1 will accept to load the splashscreen and the Boot2 will reject it.
Edit: Sorry for the delay, but here is a better picture of the TI-Nspire Color prototype external Flash-NOR chip:
It seems to be a MXIC MX29SL402CBTI-90G.
Reflashing this with a patched TI-Nspire CX Boot1 will let you do everything you've allways dreamed of