I've done two in the last month. One with a load leveler and one without. Both with a boom-arm roll-in engine lift/crane. One with front sheet metal off and the other with just the radiator out (hoods-on in both cases).
In both cases all bolt-on parts were (or will be) on the engine coming out and going in.
One engine was pulled with a four-speed on it, and the other engine was pulled with the three-speed left in the truck. I dropped the three-speed before putting the engine back in. That engine was put back in place with all parts bolted to it.
There will be no need to hang over the fenders on the truck we left the sheet metal on, except for the two remote oil filter lines and the exhaust pipes.
Either chains or straps can work fine. But there is no reason why chains require that the engine be stripped before it is returned to the truck.
Tim