Do not use holes of different length than the pipe. Othervise the hole will be on the outside. All pipe is to be supplied with nothing in the hole, so that water, steam or other stuff can be put inside at a later date. All pipe should be supplied without rust. This can be more readily applied at the job site.
Some vendors are now able to supply pre-rusted pipe.
Flanges should be used on all pipe. Flanges must have holes for bolts quite separate from the big hole in the middle. Othervise you will end up going in the wrong direction. Do not mix the threads. Othervise, as the coupling is being screwed on the pipe, it is unscrewing from the other.