Mod Clarification
I want to clarify this. The word mod itself is slang for modification as some of you already know. However, when most people hear the word mod, they think of the rebalance mod or some kind of total conversion of the game. I am one of many modders who has modified the game without making a total conversion. For example, I made a jump hole clear from New York to the Top unknown system. The cool thing was no one else could use it but me, they couldn't even see the wormhole unless of course they had the files I modified.
Now to clarify what players mean when they fly through locked gates/holes in unmodded servers is probably someone has modified the game in such a way in which it was not a total conversion like rebalance or Epsilon. Instead it was as I like to say, "tweaking the files" in Freelancer to change a few things around.
I hope this helps in explaining why some players say they can do things on servers that are unmodded.
If you have any questions about this, please post it.