I have various situations where it would be very useful to be able to turn that flag on and off without rebooting.
I do a lot of AV installations with Pis, and recently I frequently have a situation where I have the Pi plugged into a DVI monitor and then need to switch it to an 7.1 receiver to play multichannel audio. Normally I use EDID because it's convenient, but once it has a DVI EDID then there's no way that I can find to turn HDMI audio back on with the 7.1 receiver since it doesn't send EDID. It ends up locked into DVI mode until I reboot.
I also have a RPi AV software package, and I need to be able to build some versions of it that have EDID enabled and some that don't. Since it can only be set with the config.txt file, this requires a convoluted roping of the config.txt into my Git repository.
It sounds like there's not a way to do this now, but it would be a very useful switch to add to tvservice.