I wrote a bit of OpenScad to laser cut a leather pen case

Mike, not sure with laser cut and would be curious to hear about the test. Conventionally round punched holes are stronger then the slits. Its like welding a crack in metal you want to drill holes to prevent the crack from spreading, just welding a crack can move the crack in another direction later on. Same goes for leather, when I cut slits for belt loops or such I always punch small holes on both ends of the slit, this helps to prevent tearing of the leather. Typically round holes are for thread but can work with lace too. Slits are generally used for lace. Also slits hide the stitch holes better then round holes but when lacing, round holes on the corners provide more room, being you lace through twice on corners. Depending on the stitch a straight slit rather then an angle slit is an option too especially with thread, the stitch lines up with the slit making the slits disappear almost entirely. When I lace I usually use the straight slit because I usually do a double cross stitch, single lace stitch the angle ones would work. But if it is strength you are looking for it's the stitch width that is more important then type of stitching hole. If the stitch length is too close together this weakens the leather more then the type of stitch hole, spreading out the stitch holes will provide a stronger seam. Most of the stitching I do the holes are spaced 1/8" for non critical stitches like the covering on a pocket clip where strength is not needed. I use a stitch length of about 3/16 of an inch apart for small projects and up to 1/4" to 1/2" for large projects. Hope this helps a little. Case looks good but I see what you see and I think its in the holes. As long as the leather is thinner then blue jeans, which it looks like it is, you could use a heavy duty singer, the non expensive one at fabric stores, they run around $200 to $300, and would produce smaller holes giving a cleaner look. Though sewing with an electric machine takes some practice to get the stitches straight or using a guid helps too. Best option for a project of this size would be a sewing all and a spacer wheel. I know you are trying to machine cut these so more of a small marking hole should be all you need for making the pattern, which if you lengthen the stitch length I think you will achieve the look you are looking for. Also round needles and chisel point needles can effect stitch strength too, if stitch length is more then 10 stitches per inch a round needle should be used.

https://www.tandyleather.com/en/product/sewing-awl-kit

https://www.tandyleather.com/en/product/craftool-spacer-set

With the laser, I am getting a fairly interesting cut. I am burning away a thin kerf, about a mm at the surface but about .1mm in actuality.

I think this will give me that rounded hole like a punch but the slit thickness. Also the laser dog-bones cuts slightly as it slows down for the ends of cuts.

Worth looking into closely.