I was afraid that the advent of massive textures might be an issue for some.
If you're specifying the *true* random trees, and not the line-of-5 which are available as an object for the user to place...
Well, all you have to do is see about bringing down the average brightness of the alpha channel, in small steps, until you achieve the desired smallness of trees out in the distance. In Photoshop, simply highlight the alpha channel, hit CTL-a to select all, and then CTL-u to bring up the hue/saturation/lightness dialog. Move the lightness slider about -5 steps to the left), save the image, and load a map in the FMB to see if any change has resulted. Repeat as necessary.
To check on the action of the 4 individual tree types made for the 4 panels in the AlteredBush8aTL.tga, make a temporary version with strong, unique colors (red, blue, yellow and purple, for example) assigned to each panel. The 'rainbow' of trees so built will let you easily keep track of each panel. In this way you can individually darken/lighten the alpha channel by panel, achieving a good balance in action on all four types.
One important note: If at any point you must brighten an alpha channel, do not let the surrounding black area get brighter than zero. If it does, you might get unwanted bleed outside your tree.
It really is that simple!
If not confident/outfitted to do it yourself, see if another user of those big graphics is equipped and willing to tackle it. I think it's worth the trouble...
Now, for the line-of-5 tree groups, you can get some ways toward a better appearance by simply altering the two parameters in the .mat file that I've pointed out in the readme. This should at least make those trees appear as 'softer' in the distance.
Don't be so ready to throw your hands up in the air just because you have better images. The approach will he the same. Ve haf vays to make ze tree better, ja?