All second source AMD (and other manufacturer) chips were pin-compatible with Intel chips. Compare the i386/am386, the i486/am486, etc. Even a few non-second source (e.g. the unique uArchs that came later) designs were still pin-compatible, such as the 5x86 and K6/K6-II/K6-III. In fact, the third parties were the first to break away from electrical compatibility with their Super Socket 7 motherboards.
Intel did change sockets as a means to disallow socket-compatibility; forcing consumers into their architecture if they bought their motherboard, but that had no effect on AMD's development. AMD had purchased a significant share of DEC's engineering portfolio and, along with it, their employees. Those employees then developed the K7 (Athlon) architecture around some of the Alpha's technological advantages, which included HyperTransport, a multi-issue FPU (fixing one of the major issues AMD had struggled with and bringing them ahead of Intel), etc.