The law is the law. Wishing it were different doesn't make it so. Which means that yes, Compaq and other PC clone makers may have broken the law by reimplementing the PC BIOS. The BIOS API does not depend on named functions but rather on specific values appearing in CPU registers, so I'm not sure how copyright applies to that. Maybe a "structure, sequence, and organization" argument à la Whelan v. Jaslow.
> The BIOS API does not depend on named functions but rather on specific values appearing in CPU registers, so I'm not sure how copyright applies to that
Do you have any reasoning for treating magic numbers different from English-like names for the purpose of determining copyright eligibility?