For starters, for those that don't know what a Run Through is, it is a mechanic that will remove the Found In Raid tag from your items picked up in that raid when you extract (making them not usable for most quests and not sellable on the Flea Market) and also the raid will not count for "Survive" requirements for quests. It happens because you "extracted too quickly" or "didn't do enough actions in raid".
Allow me to explain.
There is a single requirement to prevent a Run Through, gain 200 experience points in that raid. Period. The end. There is no other requirement.
Since I can already hear the keyboards typing furiously with things like "but but but, 7 minutes is all you need to stay in raid for!" Allow me to explain further.
After 7 minutes of the raid timer have ticked down, anyone that extracts gains an "Exploration Bonus" of 300 experience points awarded in the post-raid screen, thus avoiding a Run Through even if you didn't touch a single item or shoot a single bullet.
Now, since I hear even more furious typing about Player Scavs, let me explain some more.
The length of time a Player Scav has been inside the raid is completely irrelevant to a Run Through. Any Player Scav that extracts after the initial raid timer has had 7 minutes pass will gain the 300 "Exploration Bonus" experience points and will not have a Run Through. If you load into Reserve as a Player Scav, and the timer says 42:59 or below, you can instantly extract and you will gain the 300 "Exploration Bonus" experience and not have a Run Through.
The only place I have ever seen it possible for a Scav to have a Run Through is on Factory. I have witnessed with my own eyes, my Player Scav spawn in with 13:45 left on the Factory raid timer and I instantly extracted and got a Run Through. It might also be possible on Reserve, but I have never personally witnessed spawning in with 43+ minutes on the timer.
So, in conclusion. 200 Experience points gained is the only requirement to avoid a Run Through, nothing else matters. Extracting after the in-raid timer has more than 7 minutes missing from it will give 300 bonus experience, regardless of how long you have actually spent in that raid.
Thank you for coming to my TED talk.
Source: https://www.reddit.com/r/EscapefromTarkov/comments/qs9cjc/a_complete_explanation_of_the_run_through/