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Saimadhav, since you did not mention a problem with the appearance of the True/False button or the action buttons, which were issues before, I presume they are okay.
S1. For Shell, which does not have Format, alt-O opens Options. The hot key for Format should be changed to 't' so its addition does not diable O_ptions. I will do this in a separate patch.
S2. For my first patch, I see all 5 files. For -2, I only see entry for Binding.py. Odd since the only difference is the better line endings (and date stamps). When I uploaded this, it took about 10 minutes for 'review' to be added. I don't know if that is normal as I never paid attention before. Please post query. 
1. I see the problem with the text entry boxes. I will look for a fix.
2. I have always been bothered by 'Options' -> 'Configure' -> 'Preferences'. Hotkeys should be 'I' and 'E'. I think 'Idle' and 'Extensions' might be enough, without 'Configure'.
3. I agree and will delete ... both places.
4. I have not actually looked at the file written, as Ned's review and my edits focused on glitches in the appearance of the dialog itself. I agree that if nothing is changed, nothing need be written. If anything is changed, the entire file has to be written. But I agree that for default extensions in config-extensions.def, only writing the delta, as done with config-main.cfg versus config-main.def, would be good. This requires noticing which extensions *are* in config-extensions.def. Sections for extensions only in the user file must be written back in full. I will look at how saving deltas works for config-main.cfg, but I may want to make this a followup patch.
5. I reused the names from the existing dialogs (config and others), which match the button label and handler name. These are the capitalized method names I find least bad. I would also be happy to change them just here or everywhere. I don't want this to hold up this patch if there is disagreement.
6. Commenting out is temporary, purely for development.