I cut areas out of my template, and used that as a guide. However, I was using a straight bit, and bushings. This allowed me to drop my cutter just enough to remove the laminate. Using a flush trim bit would be a little more difficult.
If I were to do it again I might:
1. Place the battens with carpet tape first
2. Use the battens to place router guide blocks
3. Clamp my router guide blocks
4. Remove the battens
5. Route the laminate off
At this point you can glue you battens down.
Also, I laminated the inside first, then screwed through the outside into the battens. Once all the battens were in place, I laminated the exterior.
You're right... it is more work, but rest assured you wil have a cabinet you can park a truck on (or let a 5yr old boy loose on

).