If the mod itself allows selecting a range of values for one of its modifications, having that selection available from an in-game screen would be far more user friendly than requiring someone to modify XML or run some batch file or executable to get at the option selection within a mod.
An example: A mod that adjusts the number of zombies alive at one time within each biome might allow you to adjust how extreme each biome is (maybe from some fraction to make it easier up to some multiplier to make it extremely hard) with a slider or something like that from a custom/mod options menu in game.
The goal, as I see it, would be to allow mods to not just be "all or nothing" in their design and instead allow them to scale or turn parts of them on or off. This also assumes that TFP allows numbers in the XML to be simple formulas (variable, value +-*/ variable, or value) and that there be some way to define global variables that are usable from the XML (maybe named mod_something, for instance). Then a mod could simply have a modoptions.xml file that would list needed options and their range of values. At least that's the way I'd design it.
The way I'd set up a modoptions.xml file:
<modoptions name="ModName">
<!-- select a value by name from a dropdown list, setting mod_ModName_MyOption1 to the value of the name selected-->
<selector name="MyOption1">
<selection name="value1" value="0"/>
<selection name="value2" value="1"/>
<selection name="value3" value="2"/>
</selector>
<!-- Slider with a range of 0 to 1 with 0.1 intervals -->
<slider name="MyOption2" range="0-1,0.1"/>
<!-- Slider with a discreet range of values --->
<slider name="MyOption3" range="0,1,2,3,4,5"/>
</modoptions>
Obviously, more than 5 minutes of thought need to go into this but you get the idea.