UCSB,
When welding stainless and Cr-Mo, one will experience elongation, or grain growth in the weld and HAZ. This is not at all uncommon. With the stainless and Cr-Mo it is unlikely that the steel will contract back to it's original size. Once the molecules "stretch", or elongate, they pretty much stay there. This is quite typical of stainless steel especially. You are right, that is exactly what the gap is there for in the first place, the elongation, or grain growth due to the high heat encountered during the welding process.
CM