Ships shouldn´t be easy to reoutfit. It breaks the immersion!
I´d rather go for a timer-solution. Like... when you want a new/used modul installed, it takes time to a) remove the old one and b) fit the new one. They could even make it cost something, because I´m sure those people won´t work for free. How about adding different skill levels for these workers? The faster they do their work, the more you pay?
They could even add a random +/- on the timer for when everything works better/worse than anticipated. Such immersion, much wow, very elite!
I understand what you're saying here but unfortunately not everyone has much play time.
I think it should be in the game. And immersion-wise, if I was on my way from a cargo trip in my T9 and my next plan was taking my Anaconda out, I would ring the station that has it stored and ask it to be fitted and fueled ready to go for when I'd arrive anyway.