IBM appears to believe that they are required to obtain FCC approval of the combination of wireless hardware and aerial that they ship. This is not an unreasonable assumption. However, they have gone further by preventing any combination that they have not obtained approval for from working (with the possible exception of the Lucent Orinoco - I can't find an FCC id for an IBM version of this card, and so can't tell whether it's an approved device or not).
The relevant part of IBM's submission to the FCC for one of these components can be seen here. The phrase "unique electrical connector" appears strange. As we've seen, the BIOS simply contains a list of acceptable cards. Attempting to claim that this is "secure" is also strange, since any hardware manufacturer (or even a technically competent end-user) who wished to subvert this could either modify their card to satisfy the PCI ID requirements or alternatively modify the BIOS to include a different ID.
What is perhaps more interesting is that the regulations cited appear to require that the transmitter must not allow any non-approved aerial to be conntected. The IBM solution implements exactly the opposite - they only allow the aerial to be used with approved transmitters. A consequence of this is that other manufacturers may not design cards and attempt to have them FCC approved in combination with Thinkpads without IBM's approval. This does not appear to be the intention or requirement of the regulations IBM uses to justify their deliberate incompatibility. There is, in fact, nothing to prevent me replacing the antenna in a Thinkpad with a different solution. IBM's implementation fails to conform to FCC regulations and so reduces usability for no good reason.