I wear dress slacks most days and I don't like the look of the clip hanging over my slacks. Also, because of my rather large thighs, I always have to have pleated legs, so the front of the pocket tends to hang down with the weight of the knife when it's clipped on the lip of the pocket.
As you point out, the knife tends to ride horizontally across the bottom of the pocket. This makes a rather unattractive bulge, is unfortable, and also makes wear marks on the front of the fabric if you do it all day everyday.
I also like to keep my knife separate from other stuff that might be in my pocket, and I like to keep it where I can get to it quickly if needed.
I have several pairs with the internal change pocket and it works wonderfully. But, those are expensive, dry-clean-only pants. Cheaper, wash-and-wears don't tend to have that. So, I just add it in myself.
It's a sewing task, yes, and I'm no tailor, but fortunately, since it's inside your pocket, nobody ever sees it. So, it doesn't have to look good, just be functional. I get the material by just cutting the pockets out of worn out pants that I'm throwing away.
Chuck