Shim Tub Surround for Cement Board
I've never seen a tub with brackets like that. Usually the lip of the tub gets secured directly to the framing. What brand/model of tub is that? Can you find info online? Many tub manufacturers have installations instructions that indicate how things like backerboard should be applied.

Different sources including this Family Handyman article on Backerboard around tub indicate that you should stop the backerboard 1/4" from the top of the tub lip and the tile should canteliver over it to 1/4" above the tub.

If you look at this installation manual for a Kohler tub it tells you to use 1/4" furring strips to extend the backer board over the lip.

If you can find the manual for your tub I'd go with what they recommend. If you can't, or the brackets aren't part of a normal tub install I'd contact the manufacturer of the backer board to see if it's okay to chisel out some recesses for the brackets. If you want the backer to go over the lip use furing strips and chisel out some space for the brackets. You're still going to have an issue with securing the bottom of the backer to framing since the brackets will prevent the screws from going in. I'm not sure the brackets were supposed to be there to be honest.

Also see this post on using some sort of waterproofing over the backerboard What are the pros and cons of adding a vapor barrier behind shower backer board?