Given the critical nature of your application I would have a chat with the Applications Lab Engineers at Synrad (Co2) , IPG (fiber) , Light Conversion (Femtosecond) and Coherent / Spectra Physics for UV and Excimer. This is by no means an exhaustive list.
It sounds like you want to ablate (vaporize) material rather then Pierce and Cut (burn and push material out of the kerf with air or inert gas). Many cardboards are made using a sodium silicate adhesive that is somewhat fire retardant while others are not.
You need an assist gas to blow material through or out of the cut, and in your case it sounds like it may be better to have that gas come from inside the package. I've never seen some one do it backwards.
You'd end up cutting, but then probably have to follow up with a fine spray of water for paranoia reasons,
This just does not sound like a good idea to me.
Ultrasonic Knife with a Sapphire or carbide tip might be a better idea.
Steve
Qui habet Christos, habet Vitam!
I should have rented the space under my name for advertising.
When I still could have...