Hi there, I'm probably not the best to reply to this, but I figured I might give it a go.
I've only used Tiled in the most basic of ways and it actually has quite a few features that I've never touched, so the way I'm imagining that you're using Tiled could be completely wrong. Maybe it would be worth posting a screen shot to show how you are currently setting up your map.
If I ran into the problem that I think you are having, I'd make a tileset of clustered trees using the other tilesets. Unfortunately, this might be time consuming, but if you think that you might re-use the tileset or really want to avoid multiple layers, it might be a time saver in the long run.
Here's a really rushed example of what I'm trying to suggest:
The top has four badly drawn trees and a simple grass texture, under that (to the left) shows a seamless tile made up of the four trees clustered, then a east facing edge of the forest cluster and the (very rushed) result at the bottom right. It contains two layers; the grass, then the trees on top.
As you can see; my example is underwhelming. To get the most out of this, you'd need to create edges for at least 8 directions, create some variation tiles (to make it look a little more random and less repetitive) and I'd probably do a shading layer, to make the trees look like they are actually next to each other.
Sorry for not being able to give a less time consuming answer, but hopefully this is a little helpful.