At this point I still think it is Heads and Sectors that must match. If the replacement CF is too big, I would think one could copy the original Micro Drive CF image verbatim over top of the replacement CF. One would in effect be ignoring the extra cylinders. If the replacement CF is too small, one would have to make an adjustments to the partition table.
Looking at the SanDisk product manual
, it appears to me that all of their CF cards 512MB and above use 16 Heads, 63 Sectors. They list two 4GB cards, one with 7940 Cylinders and one with 7942 Cylinders; both greater than 7936 Cylinders of the Hitachi Micro Drive.