So is having the intake charge crash into the cylinder head. A lot of our point of views is dependent on how bad the alignment is and how much smaller the intake is to the heads.
If my intake port is smaller, I not meaning a lot, just a little.
A sharp edge in the direction of flow is a much better scenario than having a transition to a sharp edge the other way. If the sharp edge is on the head, the air will simply shear off of it and follow the port wall.
If you have the intake smaller where it meets the head, you impose a big low pressure area right there and the air tries to fill in that gap. When it does, it causes eddies and such that kill flow. There are dozens of YouTube videos showing this happening. You never want the intake port smaller than the head.