I managed to get my prefabs to display in a biome (thanks @nevir & @Predatoxic - How Do Prefab!¡? - #25 by nevir) so that I could test to see what they looked like in a “real-world” environment. As @lucadeltodecso said, any unnecessary overlap on the prefab just makes it jut out of the landscape and it looks weird!
General rules of thumb that I have learned (mostly the hard way 
):-
- the smaller the connecting point to the landscape, the better it will look on the landscape.
- always, and I mean always, add some below ground details - at least 2-3 blocks, as prefabs will almost certainly be placed where they just looks really odd without it!
I’m quite pleased at how these are starting to look now…
I just need to work out how to place them more sporadically and less clustered on the landscape now!
Edit: and yes, I know my big trees are placed in the wrong biome 