The 0.01 scale “trick” in Blender works perfectly fine as long as you dont change the scale within UE. So, make sure you have the proper proportions of your mesh in Blender, and export to UE as it is. If for example you change the uniform import scale to something else… you will get again all those transforms warnings.
The only downside of using the 0.01 scale way is that, as other said, you going to find some “problems” in Blender. For example, when you create new meshes, they are going to appear with the wrong scale, of course. Things like bones will appear so small that you would think that blender actually didnt add any bone (happened the other day to me. I created 4 bones because i thought that blender was ignoring me… turned out they were just tooo small to see em :s).