Well, I've had it the other way round. Been IN a RFDS PC12 and watched a F100 jet go past 1000' below in the opposite direction. It looks pretty big and the closing speed is even more impressive...
To the OP, I would think that what you saw was probably all above board. It is just that if you happen to snag a direct under/over pass with another aircraft at minimum separation height it looks pretty scary close if you weren't expecting it!