Every engine manufacturer makes minor changes like that in a production run.
It could have been an update, they may have run out of studs or it may have been a mistake.
Either way, it didn't harm your engine, so I would think you could do the same or get a couple studs and nuts if you wanted to.
If you decide to run with the 2 studs it will be easier lining everything up and holding it in place.
Just in case you didn't know, some manufacturers recommend replacing the head bolts and studs every time.
I would think the manual should tell you if yours are like that.