As usual I'm late to the party.... but this looks to me to be simply a case of not having the piston at true TDC and being a couple degrees past it. I don't *think* it is a full tooth off. Do you know if the engine shop installed an offset key to advance or retard the cam? That would make the marks misaligned as well. The quick and dirty check is to lay a straightedge along the red line I've drawn, rotate the crank so one of the dots is on that centerline. The other should line up.
When turning the crank with a wrench only a few degrees past TDC will misalign the marks, but the piston will look like it's still at TDC. I can't stress this enough - you must know the piston is at TRUE TDC. Because the piston dwells at TDC for a few degrees you cannot be 100% sure by eye only.
Get a degree wheel, make a pointer, make a piston stop - neither needs to be as fancy as the universal ones I made (I've built quite a few engines, not just Mopar). The pointer can be a bent piece of heavy wire (coat hanger) and the stop needs to stop the piston a little bit before the top of the cylinder. Drill holes matching the head bolt locations in a piece of angle iron or square tube and weld a nut to the underside. Basic stuff. Once you determine exact TDC this mystery will be solved...
After years of working together on my race cars, my son moved out of state and and is building a Mopar of his own. I'm trying to impart my knowledge via short tutorials I call "One Page Tech" articles and did one on finding TDC. If you are interested PM me, or if others are interested I'll post it.