Some premium brands will have the immobilizer await proper crypto from the key reader. In this case the key reader is just there to read the key and pass on the message, there is no decision being made outside of the immobilizer.
Some premium brands will also have immobilizers in other places, like the gearbox. It too will await proper crypto to shift into gear.
Some premium brands will have signed CAN/FlexRay/Ethernet frames that will prevent message spoofing, though that isn't only for this situation.
Most of the time the Gateway module has a static firewall - basically fixed routing tables so only modules that need to will be allowed to talk to each other.
Finally some premium brands will have an HSM both in the key and in the immobilizers to keep the material safe.
There is a lot more to this topic obviously but the reason some brands don't have this (and other countermeasures) is simple: cost.