Just had a look at the pics again and compared it to the M25PE16 data sheet. The two traces that are visibly shared between the cardslot pads and the flash chip are 6 and 5(on the flash chip), which are Serial Clock and Serial Data Input, respectively. They connect to 3 and 5 on the card slot pads, which are listed as Serial Clock and Serial Data Input for SPI mode, which seems to work in the same serial paged manner. Long story short, the flash chip and the card slot seem to be accessed in the same way, and still be wired correctly for both pin diagrams(both flash chip and card slot).
Upside is the card slot should work in the same manner as the flash chip, downside is you definitely have to pull the flash chip off the board while you’re trying the cardslot, or it will be paging two devices on the same channel, and neither will work.