You can post hoc modify circuits so they look like doing logic A but they actually do logic B by adding new p or n junctions.

In theory, yes. In practice it is not realistic to implement a plausible-deniable hardware backdoor targeting all CPUs being manufactured while keeping the schematics and tapeout open.

While the same CPUs are even fabbed in different locations around the world.

While also going undetected for years and while none of the engineers involved blows the whistle.

In short no, you can get away with a targeted attack but nothing so massive.