Estate Rear Hatch Seal

We've had an issue recently where the interior trim to the rear hatch on our estate has been filling up with water when it rains, meaning when you open the boot it runs out from between the metal frame and the trip drenching whoever happens to be underneath...

I initially thought this might be the third brake light or the glass to hatch sealant, so taped round them all with ptfe self-amalgamating tape as a trial.  This seemed to work for a bit but the issue recurred so as a temporary stop gap figured I'd try and make a way for the water to escape (our driveway slopes so the usual central drain hole down by the lock wasn't in the right place.  I did this by cutting some small drain paths in the rubber 'stoppers' at the corners of the hatch.  This seems to have worked and has stopped water collecting too much but it still seemed to be getting in so, over Christmas I did a bit more investigation.

I now think water is getting in past the main seal on the boot opening at the top, the water running down the underside of the hatch, past the seal and behind the trim whereupon it tracks down inside the trim to the lowest point to then empty out when you open the boot.  I've therefore ordered and received a new estate boot trim from Skodaparts and had a go at fitting it today...

The trouble is I can't seem to get a neat fit.  I know it's the right part and appears to be a redesigned part with extra sealing lips compared to the one taken off but despite my current best efforts at getting it fully on, and it being well pushed down onto the metal bodywork, as far as seems possible, the inner edge doesn't seems to be covering the interior trim in places like the old one did, seems to be sitting a bit proud in places and is making the boot near a fair old slam to shut.  Time will tell if it seals properly....

So...   is there a knack to fitting these things (I've never had a problem on other cars) and any suggestions on how to sort it...   should I start at the top and work down or bottom and work up and does the seal on newer cars fully cover the interior trim?