Thanks for reporting the additional information.
I’ve confirmed that that the OTP code is incorrectly documented in the datasheet. I’ve opened an internal ticket to track and resolve this document update.
I’ve located the source of the OTP code that’s programmed on production FE310-G002 devices. This code is in a private repo. I can confirm that it does use backup1 reg as you’ve observed. I’ve asked about publishing the source code and one concern is that it uses proprietary libraries which are not published so it would take effort to port this OTP code to the public freedom-e-sdk.
I wanted to circle back to the original question of “Why is this done?”. This write to backup1 reg appears to be a SPI flash recovery mechanism counter tracking the recovery attempts to read the SPI flash ID. After the fifth failure to read SPI flash ID after power cycling the program will enter a tight loop.