Pre-cut window mats damn you to a one-size-fits-all shoe store approach. Having your own cutter allows you to customize each mat to what best suits the picture in mind, just like a serious frame shop would do for a couple hundred dollars or more apiece.
The practice I utterly dislike in this day and age is the lazy way they do it, with all the mat margins being equal. The Greeks figured out thousands of years ago that, for visual balance, you want the "pediment" - in this case, the lower mat border - wider than what's up top. That was routine practice with custom framers at one time; now they seem to be getting just plain lazy, since with a computerized cutter, it would take only a few more seconds to program the distinction.
I cut and assemble all my own frames too, and sometimes even shape my own hardwood moulding lengths. I want complete control on the final presentation. But I am slowing down quite a bit due to aging, as well as due to the skyrocketing prices of key materials like Museum board and acrylic glazing.