The dire warning is mostly for the 3A+, where enabling USB host boot mode (which allows booting from USB mass storage devices) will permanently prevent booting in USB device mode. (Maybe...see below).
Device mode is only supported on the Compute Module, CM3, Zero, Zero W, A, A+, and 3A+, so if you don't have one of those there is nothing to worry about as far as this goes.
It still deserves a warning on other models, but not a dire warning. It's still permanent, but it is much harder for that to be a problem. It will only be a problem if you are going to have situations where you will have a bootable USB drive attached at boot time, without a bootable SD card inserted, and you will want it to not boot rather than boot from the USB drive.
Although OTP changes are permanent, it looks like there is still a way to sort of work around the USB host boot mode one, albeit at a cost of losing access to 7 GPIOs or at least making them a lot harder to use. With another irreversible OTP change, you can tell your Pi to determine what devices to consider booting from by looking at 7 GPIOs [1]. Using GPIO boot mode, you could easily switch between SD card only, USB only, and SD followed by USB, and device mode, by just changing pull up resistors on the relevant GPIOs.
Burning the OTP will prevent you from starting the 3A or 4 in OTG mode; you can still do that in software by dynamically loading the dwc2 overlay once Linux has booted up and specifying the mode=peripheral parameter (then loading the kernel module).
