>>408648394
Apply transform zeros out all the position/scale/rotation values, while keeping everything in the same position. After this none of your meshes will have weird/negative scales, and your model's origin will be 0,0,0, with a scale of 1,1,1.
Blender is also weird and negatively scaled objects won't have their normals inverted until they are either exported or transform ( scale ) is applied, so doing this lets you check for that ( overlay - face orientation ). Scale is the most important thing to apply, position and rotation less so. Also do the armature. 
When you merge a mesh into another one, this is done automatically, so it shouldn't really be a problem. Good idea to Apply transform on the final merged mesh and check for issues like normals being weird though.
The meshes in your avatar having a scale of 15-30 instead of 1 once imported to unity is caused by "Apply scalings" being set to "All local" in the FBX export transform tab. Set it to "FBX All" instead, but do keep in mind that if you already have your avatar set up in unity, changing this after the fact will make unity shit itself.
Physbones values still have to be tiny, but slightly less tiny. I don't know what's up with that.
While we're at it, also disable "Leaf bones" during export; you never want them.
Remember to backup your unity project if you've got one; it's very easy to break everything.