Generally speaking,,, the cylinder align just fine. As noted,,, the cylinder gap is the normal issue we deal with. And use a range rod if you choose to check it.
MAKE SURE the gun is unloaded.
Use a properly sized brass or wooden rod for a range rod.
Cock the handgun.
Stick the rod in the bbl,,, and check to see of the rod sticks any when it starts to transition from the barrel to the cylinder. (You can mark the rod with the barrel length to watch it more closely.)
Check all 6 chambers.
Now,,, if a properly sized rod isn't available,,, use the largest sized rod you can get that will still fit in the bore. Mark for length. As it gets near the mark,, make sure the rod is sitting flat along the barrel and gently push it towards the chamber to check it. I do this with a gun in a vise. Next,,, rotate the gun 90 degrees,, and repeat. I do it on all 4 90 degree points. By allowing the rod to sit flat in the bottom of the barrel every time,, I get it flat & can see if it bumps the chamber.
A light improperly used,,, can give you a false shadow & make you THINK it's not aligning properly.
And WHY NOT use a 9mm in a Vaquero?