If I was to buy a flat worth in the region of £1 million for my 17 year old son on top of our house worth roughly £800,000, how much capital gains tax (CGT) would we expect if we just bought it straight as a second property? Also is it possible to get a rough estimate of how much CGT he would pay if we were to buy it via a (bare?) trust with his CGT annual exemption, and (perhaps) lower tax bands?

I think that there is a basic mistake here. There is never any CGT for a purchaser when he purchases an asset, only for the seller. If, however, you bought it for your son (in his name) and he lived in it as his main residence (e.g. while a student in university/college) and then sold it when he decided he didn't want to live there anymore, then there would be no CGT on sale due to principal private residence relief. You would have to make sure(!) that you lived for seven years after buying the flat in his name, so that the £800,000 is not included in your estate, for inheritance tax purposes, when you die.