I have this same problem and compensate by turning the volume WAY up on my stereo
I've noticed on my car, and read somehwere here, that other seals can be modified to fit on the targa top sides. Mine has one that is closed off at the angle cut on both sides, then one that is not - suggesting that a longer seal was cut and made to fit. A while back I googled VW seals and there are sourced for cheap standard seal, with diagrams of the internal seal profile. Some day I will get on this project too. I was thinking that if the mounting hardware for the side seals could be tinkered with, maybe adding washers or tearing out and re-glueing with a 1/8" spacer underneath would seal the gap. Keep us posted on any progress - I'm sure your not the only one with big gaps on the sides. I have to cover my car every time it rains (every day lately).