Can I cut a hole and add a drain or pipe through the liner?

Yes, you can cut this liner just like any other flexible liner. The easiest way to add a drain is with a bulkhead fitting ( https://www.everything-ponds.com/bulkhead-fitting-threaded.html) or a dedicated bottom drain fitting 

For bringing a pipe through the liner, we would suggest using a bulkhead fitting along with an MPT to Slip Adapter Male Pipe Thread Adapter MPT X SLIP.

If your pipe or pile is a non-standard size, and you’re unable to use a bulkhead fitting, we can create custom-sized Pipe Boots to fit.  

Other penetrations like skimmers can be installed using the manufacturer's recommendations.