I use the PC-E lenses and on my 300/700/800 and have simply learned to live with it and I'm quite happy. Even happier when I need a flash for fill or to trigger remote/ttl flashed and I don't have to have another cable, wireless controller or other device.
IMO, like video, that flash is simply another tool for my use that's there for me if and when I need it and can be ignored when I don't. When I found that I neither needed a flash to control my remotes, a PC cable or a wireless controller back in the days of my D100/D200 years ago, I didn't even want to consider going back to a pro-series Nikon and resisted upgrading to a "pro" body for several years. For my commercial/event photography and travel, that little and annoying built-in flash is a godsend!
Until the 7D, Canon didn't even have built-in ttl control, thus for my work, Canon had not what it took for my lighting. Though today the his ISOs and LED lighting is lessing my need for my wireless TTL, that flash still is a very viable feature.
But, as usual, your results will vary...