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Reason I ask is because of how modtek loads mods. It appears it loads them alphabetically and then adds on all the other disparate entries from other mods and recompiles them into one list. So... alphabetically that's important.
 
In mod Tek the load list is now editable so you can control the load order.
 
If two changes to the same base vanilla file conflict, the last one to load take precedence.

How it affects "order" for the shop question at hand, I'm not sure.
 
Shop order for mods loading in Mod Tek shouldn't be an issue. The store files are in JArrays so you can't piece them together. You must define the entire JArray. Which ever mod defines it last will win.