I ordinarily ask them not to bring the unwanted item, but with grilled tomatoes, I know I can put it on my husband's plate and he will be even happier with an 'enhanced' breakfast.
The one exception was The Pippin in Maidstone: asking for my burger with "no bun; everything else, just no bun" brought
just the burger, no everything else, no bun.
Took a while for us to go back [we're English, don't you know; we don't do complaining easily or well, and we'd already waited ages for service and even more ages to be served food], but when we did we took note of the server...
Ditzy woman [she'd been ditzy at repeated visits, and never seemed to listen]? Yup, they can waste my bun after I've scraped all the good stuff off and eaten it. Manageress or the guy behind the bar? "No bun, please but everything else" and that worked fine.
We got to the point before we left Maidstone, that if DW was the server in the restaurant section, we'd just go cook food at home, and try somewhere else at the weekend. Oh, how nice it must be not to get churned up by the thought of having to (repeatedly) ask for what you ordered!