Imagine 2 mods change the exact same thing (for instance, mod 1 changes NPC X speed to 50, mod 2 changes NPC X speed to 60).
And what about text changes (for instance, mod 1 changes NPC name to "John" , mod 2 changes NPC name to "Jack")?
It seems to me you need a ordering rule, why don't use the standard (mod timestamp)?
Doing an average or anything like that is likely a bad idea. There are mods that FIX weight, armor values, weapon damage, Ect. I think there's a couple that lower the price on over-priced items. So assume a newbie writes a new dagger, that does 4-10 damage and health of 1000, and priced it at 10000. Another mod says the price was too high and fixes it at 250 and bumps the health down to about 300, do we go for the average of 5102, and 650?
Text changes are just that, changes. I am not able to merge raw text in any way. The mod makers should be doing a well enough job with their updates on text to not worry about that. And usually updates tend to be minor fixes or re-writing the same thing from what i see, to better flavor the plug-in. If the second plug-in changes his name to 'Jack' then i hope he updated all references to jack's name (if any).
I'm hesitant to use the timestamp(s), however for the --load_ini i may just have to. There are cases where merging one particular mod is better after another, even if it has a earlier timestamp. I don't want to worry about updating the timestamp(s) to just pass the other one so it doesn't go out of order, assuming the order even matters for that plugin. Besides, not only would it break the mods and game i compile for myself, but the implementation becomes more complex and can't be controlled, likely not even with --input.
And don't forget, the stronger part of the program for merging, doesn't replace or do whole records, instead it works by subrecords, and if those have multiple parts, sub-parts too. Example WPDT is the weapon Data, and has about 14 fields. Other mergers can't handle that, even if they could handle separate subrecords. That's why order becomes a bit less important, except for certain cases.