Certainly. But even those can be routed so that the WR signal for a particular address also doubles as half of the AND input which causes a read from another range to always return zero, for example. (That's not an "undocumented opcode", of course, but it can be used maliciously). It's certainly not easy to do this kind of meaningful obfuscation though, especially between different blocks, since different blocks are usually in different clock domains, too.

Edit: sorry, my neurons got all jumbled and I was thinking of a far more general case, i.e. undocumented behaviour in general, not just undocumented instructions. Indeed, only a relatively small subset of all these transistors is relevant in terms of undocumented instructions specifically.