In the link you provided the picture shows a 3 spool but description says 2, just FYI. I wouldn't recommend cutting a welded cylinder just to re-clock the ports. You could use a tie rod cylinder and clock the ports as you wish, but a welded cylinder is generally going to be more compact and stronger. If you absolutely can't find a port configuration you like, it would be easier in my opinion to plug the existing port and drill a new one where you want it. A lot of times aftermarket cylinders will have two ports 90 degrees apart on the base end, and some will have it on the rod end too.
As far as a relief valve I wouldn't worry about it. You would likely bend the thumb or break your pivot pin long before blowing out cylinder seals.