Imported Mesh not in the right Rotation/Alignment

Hello,
I have been making mesh for a few days now and I noticed that when they are imported, they are on their side (90 degrees). When I click and drag them into my scene, they take their proper rotation and no big deal. However, whenever I try to use a Prefab Brush or any of the foliage/tree painting tools that come with Unity, my meshes revert back to their sideways state and go super super tiny. For the longest time I just thought the tool wasn't working until I saw tiny little specs, on my grass, which happened to be a small forest lol.

I am using Blender. I have applied Rotation/Scale/Location before exporting. I even tried this fix I found online, saying I needed to rotate the model on the X axis by 90, then go into Object mode and rotate it on the X again by -90. Nothing seems to work.

Here is a screenshot of what I am talking about. The trees on the ground are only that size because I had to manually change the scale afterwards. But if you look at the trees standing up, same model, they import scaled just fine.

 

Unity is Y-up working space. If I remember correctly Blender allow users to setup either Y-up (Maya) or Z-up (3dsMax) references. If you are in Y-up space, just reset XForm. If you are in Z-up space, I'm not sure in Blender but 3dsMax allows users to affect pivot only to rotate the object pivot X-axis into 90 degrees after resetting XForm. Hmm... Maybe you can use this Blender plugin which does similar job as "Affect Pivot Only" in 3dsMax.