Handle the BOM however you want, but please don’t remove the “red dot”!
It’s extremely helpful in pinpointing non-displayable characters, or unwanted ones (like the BOM).
I sometimes have to use characters like the zero-width space, zero-width non-joiner and -joiner, word joiner, zero-width no-break space etc. and it is really helpful having the “red dot” in edit mode to show “here is something invisible”!
Same with the BOM: It is neither needed nor wanted here, so current status is a good signal for me to get rid of it.