Just a few things you might also want to try.

First make sure your rebuilding the level after applying the code from wiki to your tree models.

Second make sure the level is being saved as the correct file name.
In other versions of wed... Not sure with the new beta. Levels would sometimes be loaded with a ~ appended to the file name. Ussally when just opening the level from the list of recent levels under the file dropdown list.

Look at the top of wed and be sure the correct path and file name are there and it doesnt have ~ anywhere in it. If it does simply go to file>save as not just save and overwrite the original file name. This has caused me to loose my mind in the past. Rebuild then try again.

Also I would do as said above and get a tree model from loopix's site. I have used all his models and they work great with the code from the wiki. Some of the best trees ive ever seen.

As for loading the level with a simple script instead of the templates you could create a simple function inside your main wdl file.
Code:
 
Function Main()
{
  freeze_mode =1;
  level_load("level_name.wmb");
  wait(3);
  freeze_mode = 0;
}

where level_name.wmb is replace with the name of your level of course.
Then you should just be able to press 0 to move the camera freely.

As for alternatives... The only thing i can think of tho it will look nowhere as good. Would be to open your tga file and save it as a bmp or just get rid of the alpha layer entirely... Replace anything thats suppose to be invisible with pure black 0,0,0 and set the models overlay flag to on. This will make all black areas of your model transparent but will also likley leave ugly black outlines at the edges of your leaves. Tho I dont think theres any sorting errors with this method...

Really hope you can get the problem figured out. I know its gotta be something simple... Too bad theres not a 3dgs geek squad that will rush to your house when your having problems

http://www.freewebs.com/otama_syndicate/index.htm - Each master to his own technique.

- Not me said the bee, Nor I said the fly.