I think OpenELEC should allow you to edit the files with the default root/openelec combination of username/password.
As for other types of OSes like Raspbian and RetroPie, you’d need root permissions to edit the file.
In order to login through WinSCP as ‘root’, you’d first need to set a root password. You can google how to do that.
Or you could login as pi/raspberry with SSH or your preferred method and then edit the file with nano: $ sudo nano /boot/config.txt
I have tried all theese options, but they all failed due to write protection.
I hope that there is something that I have missed, that some of the experts here have knowledge of =)
I have never had a problem mounting any of the OSs and configuring the config file.
For Openelec I use these 2 lines in ssh after login:
mount -o remount,rw /flash
And for Raspbian and Retropie I use this one line:
sudo nano /boot/config.txt