It's not necessary to reflash the bootloader to use a new system image, and, as you suggest, not a good idea. None of the partitions mentioned in the article contain the bootloader, including the potentially confusingly named "boot" partition. Instead it contains what the bootloader (or SPL -- second program loader) boots.
If your phone already has a fastboot compatible SPL (the ADP1 mentioned in the article does), there is no need to change the bootloader, and you can flash newly-built system images, or backups of your old images at will without (much) fear of bricking your phone. When I want to try a new image I've built, I use nandroid to back up my phone in its current state, then fastboot to flash the image, and if it's unsatisfactory, use fastboot to flash by nandroid backups back.
Typically, part of the process of liberating a G1 is to replace the SPL with a fastboot-enabled version.