For that project, I used a really long 3/16 bit on a slight angle, baffle was 1.5" so had lots of room. If you found the right combo of bit/ right angle drill, you could do it that way as well which would keep the holes straighter. That being said, the angled holes weren't noticable when it was all done.
Keep in mind, when you go from inside the cabinet (basically upper sealed woofer, you don't have to from inside that woffer cutout... you can go anywhere near the top of the baffle inside the cabinet up to the lower MTM woofer cutout.
Then just cut small slot arouind the inside of the lower MTM woofer and the tweeter to get the wires up to the tweeter and top woofer
jay