I'm gonna reply myself, since I have found a way out to solve this.
I actually changed the big tree brush type (under attribute editor> Brush Type) from [Mesh] to [Paint].
I had already noticed that there were differences between my two trees specially regarding Anti Aliasing.
I also had to crank up the Stamp Density from 3 (default) to 6.
Now I think it's more clear for me when Paint Effects uses Stamps ([Paint] Brush Type) and when it uses something like geometry ([Mesh] Brush Type) (I don't know if they are actual polygons since they are not converted). But the difference between both methods is very clear when you see the result.
Since both trees are made of Stamps, the artifacts I showed last post are now gone. Maybe there's something that don't work well when using Paint Tree in front of a Mesh Tree, Flow Animation, Maya Software, and stuff...
I also noticed that when using the paint method, the tree shading seems to be slightly different, but I'll deal with it, no problem.
Hope it'll be useful for someone as it was for me