Thanks for the useful thread.
I needed to do this on my pre face-lift mkiii estate. So I decided to give it a go and thought I'd post my experience. I'm a low level DIYer, and that's in the house. Cars, forget it. But what's the worst that could happen?....
Anyway, it turns out the advice here is good. I would say that the front doors are a bit tricky because you have to slide the seal under the wing mirror, and really it's a bit big and the end cap can get mangled. But by applying a little bit of silicone lube, teasing the end up and lifting the mirror away whilst iching the seal under it I could get the job done. That's on the drivers side.
However I tried the passenger side first, without the lube, and without lifting the mirror. Brute force works, but it did bend the seal a bit, and thanks to the metal retaining strip built into it it now has a little lump in the middle of the door. My bad.
Of course you could eradicate the risk by taking the mirrors off, but that sounds pretty involved and I couldn't be faffed with it.
Anyway, I hope this helps anyone else who decides to give it a go.
I ordered the parts - all 4 outer seals - from the skoda-shop place in czechia and they were helpful with making sure I got the right bits. Cost about £75 delivered by fedex within a few days.