The pride of the xServer/xSeries systems were "complex" setups -- multiple chassis -- with up to 32 sockets, and 512 GB of RAM. These required a lot of IBM internal engineering, where they made pin-compatible sockets for what Intel was offering at the time, and glued those chips into _hugely_ different topologies than Intel had in mind.
These systems sound small today, but back in 2001, this was a really big deal for x86. The IBM-proprietary chipsets were much more expensive than off-the-shelf systems, but still a fair bit cheaper than going with NCR or Unisys, competing vendors with proprietary x86 MP designs.
IBM had a lot at stake when that socket changed. Achieving pin-compatibility is hard! Intel is very jealous of their documentation, and prefers to offer paper only, with water-marked copies. It's like owning a gutenberg bible. Engineering something pin-compatible with an Intel x86 CPU has never been easy.
It was no doubt worth it to their "big" x86 server business to ask Intel to make a special run of chips with the old socket layout, but the new emt64 extensions. I bet it was a complete no-brainer compared to the costs of integrating a new socket!