Dan,
There are two schools of thought here. The one is to add the setting to the Options page just like the HTTP port to be an integer number between X and Y. This way is simple and without any fuss. The second is to make the part of the config file that you need to edit manually. With this option you save on the Options Page space but then it’s a manual thing to edit. Fortunately it’s a static variable and once set then it will probably not change for the life of the Pi.
So, both have advantages and disadvantages. I would say stick it in the Options page and see what the reaction is from the community. My suggestion is to put it next to the ‘Use RS’ checkbox. If checked, then enable/make it visible, if unchecked then either disable it or hide it.
And… You could use either a textbox or a dropdownlist for GPIO pins.
Ingo