(Yes, timing chain, not primary chain) It's just like any timing chain replacement. The crankshaft position and the camshaft position control the pistons position and the valves position. The thing that makes them NOT collide is the timing chain, so you can assemble the top end safely, but it wouldn't be stupid to use the old timing chain temporarily, just to maintain the correct relationship between piston and valve positions.. Then, when you get the new chain and tensioner you just change them... Make sense?
If you couldn't have the top end assembled to change the timing chain, then every timing chain replacement would require a removal of the top end....