Flanging does not mean you will automatically have rust problems down the road. There is a greater potential for rust compared to butt welding, but it needn't summarily be dismissed. I certainly wouldn't do it where you can't get to the back side. And, a rookie welder doing butt seams in sheetmetal can quickly end up with a warped mess.
What can't be argued is the necessity to remove cancerous metal (corrosion that goes all the way through the metal - even if it's not readily visible). Covering that up will result in bubbled paint and more rust in short order. So whether you replace an entire quarter (which is not always the best thing to do) or simply cut and patch the damage will depend on time, budget, and the value of the car.
The only reason I replaced the one quarter is because someone had replaced it once already years ago following a wreck! They cut out the damage, lap welded the seams, them beat them down before lathering bondo on. The wheelhouse was still crinkled and no attempts were made to seal anything so water got in and rotted it. I cut out some rot behind the driver side rear wheel and butt welded a patch in.
Panel bonding or a combination of bonding and welding is worth considering. There is the potential for bond-only seams to ghost through the finish as it expands and contracts though.