Pixel devices are A/B partition layout - meaning that the critical partitions (/bootloader, /radio, /boot, /system, /vbmeta, etc) all have two slots - /boot_a and /boot_b. Normally, when you flash the factory image, it just flashes to whatever is currently the active slot (you can see this at the bottom of the bootloader screen). Sideloading the OTA on the other hand always installs to the
other slot.
The A/B layout is used for
seamless system updates - while the system is running on one slot, it can download and install an update package to the other slot, then schedule a reboot to that slot, so that the only "interruption" in the user experience is the reboot.
Example: You're currently on slot A, running the September update. When the October update comes available, the system can download and install it to slot B. Following a reboot, the system boots slot B, so you're now on the October update on slot B, and slot A becomes inactive. Then, when the November update drops, the system can download and install it to slot A.
It's generally not necessary to flash the factory update to both slots.