@m2design: I added a new render function "transparency = 8" This will allow you to render transparent object before the water plane , and your building should then also display from below water , give it a try, and let me know if it works
I have not mentions this option as it is not really something that should be in the fpe, but should be a per object setting , but for now you can use it in the fpe. in the future this should be a artist choice when and how a transparent object is rendered, so we can cover any kind of possible placement.
About water and vegetation , as cybernescence say this was a render issue that was fixed , so it is now possible to have vegetation below water, GG will still remove the vegetation below water. This fix was made to make cybernescence's vegetation changes work so when he submit them to GitHub they will work and let you have vegetation below water line without GG removing it again, hope this explain the change
As cybernescence has been so kind and offered to submit the changes to GitHub there was no need for me to also make that.