I don't remember (or never knew) the size/pinout, but could the extra socket be for a PMMU chip? If the upgrade was designed to work with either a 68030 or a 68020, then they might have provided a socket for the PMMU, for the case where one is using the 68020. And naturally the socket would always be empty when using a 68030.
The PMMU would have been a 68851.
I find it interesting that jsarchibald's board is missing a forty pin chip and supporting chip next to it, but CJ's board has those two. CJ, what are the markings on the chip in the lower left corner? Forty pinners like that were often serial controllers (85C30), floppy controllers (SWIM or WD37C65), or SCSI controllers (53C80). No reason why an SE would need any of those though.
Perhaps this upgrade is meant to be usable in more than the SE, or versions built on the same circuit board... A 128KE or 512KE upgrade might benefit from having a SCSI chip on board.
The PMMU would have been a 68851.
I find it interesting that jsarchibald's board is missing a forty pin chip and supporting chip next to it, but CJ's board has those two. CJ, what are the markings on the chip in the lower left corner? Forty pinners like that were often serial controllers (85C30), floppy controllers (SWIM or WD37C65), or SCSI controllers (53C80). No reason why an SE would need any of those though.
Perhaps this upgrade is meant to be usable in more than the SE, or versions built on the same circuit board... A 128KE or 512KE upgrade might benefit from having a SCSI chip on board.