A quick update. This did get rid of 90% of the noise, but occasionally it still came back. So I removed the rubber strip completely to clean it all up and stick it down properly and I think this revealed why it's making the noise.
When I re painted the car, the paint pooled onto the rubber section, creating a hard section that would tap onto the body which made the annoying sound. So really, it's my own fault for doing a shody job on the paint job, but at least I'm fixing it properly now.
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