There are ways to make the reproductions seal. I noticed the holes are slightly off too but got them to thread in. It might be good to enlarge the holes by a few 1000ths.
On a dry case, out of the car, begin by running a very tiny maybe an 1/8" bead of The Right Stuff sealant around the INSIDES of the holes of the new pan. Align the cork gasket & Bolt it LOOSELY SNUG to a clean, oil-free trans case and let it cure overnight.
The rest is self explanatory but clean off any RTV you see that may have pushed out the holes.