SH5 is totally different in this regard, but in SH3 I have never seen increased enemy traffic in my assigned mission quadrant or anything special not happening outside of it. They are just orders given to you and it doesn't matter gameplay-wise I think.
That beeing said, with some special mods it may be that you are sent via radio messages to some location with enemy units , this is much more of an opportunity (but chances are I'm confusing it with SH5 which I play a lot recently).
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