If the head holes are ending up low relative to the intake holes, that is what you want! The intake will move downward as you torque the bolts in place and compress the intake gaskets. If the head holes are in the near the top of the intake holes when you start, then the bolts may bind in the intake as it tries to move down during torquing and prevent the intake from clamping the gaskets properly.
We had the exact same type of alignment with our Edelbrocks and a new Edelbrock intake, and had to wiggle and fanagle the intake bolts and push down hard on the intake to get them all started. But they torqued down and you can be sure the intake did not bind. I can't remember who said it here on this site before, but they had someone stand on the top of the intake to press it down to get the bolts started LOL.
In your case, I'd be more concerned with the rear of the intake moving down when torqued and the bolts possibly binding on the intake. (Probably not an issue, just a concern.) As for machining, as said, the intake surfaces may be tapered front to back on one side or both.
Are the head bolts all in place, and snugged in place here? If not, then things are going to move some more and your intake fit right now may not be right. At least have all the head bolts in place with maybe 10 ft lbs torque to make sure they are aligned as close as they can to where they will be.