Quite possibly you can do something about this, it all comes down to space. Not the space you can see, but that which the game sees. Imagine every item in-game is encased in its own box, this is known as the Bounding Box. The idea being, if two such boxes collide (share the same space), the game will prevent one or the other from showing. When making a model for SC4, by default this Bounding Box will encompass the fullest extremes of each edge of the model. But trees especially have lots of parts that stick out, only the trunk really needs its own dedicated space.
Every Prop or Buildings Exemplar has a property, "Occupant Size", this represents the size of the Bounding Box. However we can alter this property, making the reserved space of a Prop / Model smaller. For trees, in fact I use this for almost all props, .5,.5,.5 is a good setting to use. This means an object reserves only 50cm of space in width, height and depth. You know in the Lot Editor, those Yellow or Blue boxes you move around, they are the same size as the Occupant Size. So when you see big squares overlapping each other, you can see that the Occupant Sizes could do with some tweaking.
Simply open the Prop Exemplar in Reader, find the Occupant Size property and edit it to the aforementioned .5,.5,.5 for each of the three values. The one problem is that this information is "embedded" into a Lot when you make it, it's not dynamically read from the Prop. Put simply, that means in order for the changes to have any effect, you must re-edit the lot by removing and replacing any Props where the Occupant Size was changed. Having done this however, you should find the game more forgiving in terms of the space it can make use of.
You may have read about making Lots more MMP friendly before? Essentially this is how it's done, reduction of the Occupant Size gives more free space to work with. There are some caveats to consider though. First, Occupant Sizes and Bounding Boxes are there for a reason, you wouldn't want two buildings sitting in the middle of each other. Second, Bounding Boxes are absolute, they can not be changed without re-making the model, if these collide, editing the Occupant Size may prove ineffectual. Sometimes it takes some trial and error, but not every Model will benefit from this approach. However for trees, I'd be reasonably confident you can make improvements.