Question on file structure

[HEMISENT]

This may seem like a stupid question but here goes.
using the mod enabler
In an unmodded game the file structure is pretty self explanatory
(using Sim.cfg for example as it is commonly and easily changed)
the structure reads: data/Cfg/Sim.CFG-the game reads the Sim.CFG.

Now lets say you enable a mod like RUB1.45
the file structure remains:data/Cfg/Sim.CFG but there is now a file called Sim.cfg.RUB1 stuck down in the bottom of the Cfg folder

Lets say you then enable another mod such as Airpower
Now you have files that contain both Sim.cfg.RUB1 & Sim.cfg.Airpower located in the bottom of the folder

Which file is the game actually reading the one labeled Sim.cfg or the latest which is Sim.cfg.airpower
I'm assuming that the enabler is just re-naming these files so they go back in place as they're disabled one by one