That's really strange. Thinking about the construction process, I highly doubt that they pre-drill the toilet connection in those tanks until they are ready to install the toilet. I'm guessing they mount the tank and then to install the toilet, they use a hole saw right through the floor and into the tank to make sure the alignment is correct. It would keep from having to measure precisely.
Any way you can check to see if the vent pipe is installed correctly?
Mark, Jenny, Adam & Lucy
2013 Rockwood Roo 233S
2015.5 Silverado 2500HD CCSB with Duramax/Allison