I upgraded from a CM4 with WiFi and eMMC, however I never booted it from the eMMC module. I upgraded to a CM5 module with WiFi and eMMC. I do not use the eMMC storage at all. I have a 1TB NVME SSD, which is much more reliable and performant than the eMMC drive.
If the CM5 finds no bootable operating system on the eMMC, it will then attempt to boot from the NVME drive. This is similar to how most PC BIOS systems will try booting from USB, then CD-ROM, then a SSD/HDD, and finally the network. The RPi also has a boot order that it uses. As long as the eMMC is empty on a CM4/CM5 module, it will skip over it and try to boot from the NVME drive.