Engineers who hold type ratings/approvals on type can also hold a company authorisation to c/o EGR's (engine ground runs). It can be idle only or full power.
We have to do simulator checks every so often, during these checks all sorts of problems are thrown at you to ensure you can cope with the problem and deal with it in the correct manner.
As Dave says the a/c will have it's park brake set and chocks will be positioned at the main gear.
Occasionally take off power checks are required hence the use of a run bay, the reasons for this can be many, component replacement etc. It can be enjoyable if everything goes as it should, I've only ever had 1 engine fire for real in the 30+ years I've been doing it, that was interesting.
When running 747's at high power you have to balance an outboard engine with the same position on the other wing, although not to take off power there is a lot of thrust being generated, it can get a bit bumpy at times.
The only time I've had to shackle an a/c down as you put it, was many years ago in the RAF when we ran Harriers, you had to check the nozzle movement, the shackles stopped you going straight up.
As for getting on the flt deck when this is going on, almost if not totally impossible in this day and age I'm afraid..