While I have no experience maybe if you can fold the rubber in half and use a hand held paper punch (also positioned to cut half) you wind up with a round hole once cut and straightened out. Otherwise burning a hole with a soldering iron..., maybe. I understand your concerns about tearing and a smooth hole would help that. Could be they are just intended to glued on.

And those new seals aren't cheap either.  I have a wagon and have tried a number of rear hatch seals that looked like they would work..., but didn't. We use have  two self serve yards but the independent yard closed. They charged $3 for any door seal and it was reasonable to experiment.  The remaining yard is a corporate Pick Your Part. They have ambiguous terms, pricing and charge by the foot so the same part there is $15+.

Regardless I've found some vehicles seals work well in other cars.  My '64 Studebaker does well with door seals from 1st gen. Madza MPV's.  I had a Plymouth Belvedere that worked well with the Mitsubishi based Plymouth Sapporo door seals (try finding those today.  I haven't search for seals for the pinto doors - yet.  I did find decent wagon rear side glass seals a while back and swiftly got those ($3 each).

All the best, hope you get it worked out.

Glad to hear it worked out!