Custom Tree Structures taking over each other

Yes, and I've had an unholy amount of experience with this particular issue. You'll need to make a specific generation condition for your trees, which specifies something along these lines:

• There shouldn't be water above the selected location.
• At least some of the surrounding blocks should be solid.
• There should be air adjacent to/around the trunk. (You could also check for sky access to prevent tree canopies from colliding, but leaves don't count as solid blocks, so air is generally better.) 

Make a procedure that returns true if your desired conditions are met, and false otherwise. The more specific you make your condition, the better it should work, but the higher you'll have to turn up the generation chance to get a decent amount of trees. Generation conditions can also have lots of unintended consequences- if you make something require a lot of flat terrain, for example, you won't get a decent amount on hills. 

I recommend using the 'check for block in 6*6*6 box' procedure template, which you can also configure to just check the world-surface, (remove the y component), if you're doing something like trees, as this is much less performance intensive.