Not sure about stock locations side to side wise, but:
If your engine is centered and the transmission is offset to one side, the transmission mount is offset. This puts the engine/trans in the vehicle crooked.
Doing a swap, pretty much everything is variable, but the power train should be straight in the vehicle. The engine may be offset to one side or the other, but the whole engine/trans/Xfr case assembly has to move, not just the engine. If the crank snout is centered in the frame, then the trans output should also be centered. It may mean you have to fab a trans or Xfr case mount to make it line up but that's what you have to do.
If the stock trans/Xfr case mount has an offset, and you want to keep it in the stock location, then you need to offset the motor to match the offset of the trans.
A lot of motors aren't centered in the frame rails, for a variety of reasons, but they are always straight(parallel) in the frame.
Hope that helps
"Never attribute to malice that which can be adequately explained by stupidity, but don't rule out malice."
My other car is also a Jeep,.. and so is the other one,.. and that one too. How many do you own before it's "a herd" ?