I believe the fine is applied if you fail the mission - e.g. you run off with the materials you are meant to be transporting. (Well that's how it worked back in the Betas - but I've not actually failed any mission in ages due to the timers being made much more lax in gamma and release).
Yeah - in the early betas it was so much fun doing high paying missions that had 10 mins. or less to complete. you really had to know the route and pray you didn't get interdicted.
No idea why that concept has disappeared for the boring stuff we have now. I used to sit at a station and accept multiple missions until one of the time constrained high pay ones popped up, then run like a bat out of Hades to get them done in the right order and get them all done on time. you were always up against the clock, but the pay out for getting it right was worth it.
Yeah, there are a lot of new features, but I often think back to the early beta days and ask myself if the game was actually more fun back then...
Certainly it's different now, but more fun?
Maybe, maybe not...