Hi Greg,
Interesting! I'll bet part of why you're going to the expense of building, rather than just buying, is because you like the area and there's ABSOLUTELY NO WAY you'd buy anything with that much room for cars!! We were only looking for 4 cars' worth in total, and have seen nothing come in the market (which wasn't just a knock-down on a slightly bigger block) in the last 5-6 years.
Our front garage is only a standard height ... let me think, it's about a 600mm step-down from the ground floor which has 2750mm ceilings ... so 3350 or thereabouts (that 600mm may not be accurate - can't remember with 100% certainty). External detached garage is 3800mm (should easily fit a car on a hoist as well as a car under).
You must have enough space on the block for a decent-sized single-story? If it's double, I'd need diagrams to understand your dilemma, as it should be possible (somehow) to get a decent-looking roofline if (at least part of) the garage section has a nearly-flat Colourbond roof.
Also, with getting rid of your own trees; that's OK under CDC, we've done so. We got council permission to remove first (3 of them were close enough to the house that no permission required, 1 is a rubber tree which also needs no permission, leaving us with two which we'll have to re-plant when finished), and then the build itself is under CDC. I know nothing about those neighbour's trees with respect to a CDC build ... and also, CDC doesn't allow you to go over 8.5m in total which might represent a PITA if you're trying to get a two-storey house with a neat roofline that matches a high lower level (our original plan for a 3.8m attached garage would never have worked under CDC, not without a flat roof - whatever they call that type of roof apart from "leak-prone" ).
Hrm, another thing about CDC is that, given your block must be a good size, 600sqm - 900sqm allows a 60sqm external garage & 900+sqm allows a 100sqm external garage. I know that'd completely rearrange your plans ... but could you get by with a normal-height attached garage & a big detached one (3-5 cars) with the raised internal height?