Any CO2 laser should be able to cut the holes. The main challenge would be the critically accurate feeding system.
There are many Chinese companies offering Roll-To-Roll systems, but usually, they are meant for cutting fabrics for large-scale production. Most likely you'll need a custom system engineered specifically for your needs. Of course, this would be quite expensive.
If you intend to build the feeding system yourself I'll suggest researching the galvo-head options.
Another idea - Instead of making an ultra-accurate feeding system you could first print the holes with any printer that works with rolled paper and then cut the holes using camera auto-detection.