Don’t worry about that eyebrow above the heat crossover. It should be exposed.
I wouldn’t slot the bolt holes IF you are doing it to get the bolts in (not withstanding that the angle is different) because if the bolt holes in the intake are higher than the bolt holes in the head, you need to mill the intake manifold to get the holes lined up.
If you slot or oversize the holes, you may get the bolt in, but the ports in the intake won’t line up with the ports in the head.