I set the unit scale to 0.01 at the start of the project in blender. Then I import the unreal mannequin into the scene. This serves as a reference for relative size for my character. I make sure the mesh of the character and the armature is individually resized so it is correct with regards to the mannequins size. Then I apply all transforms on both objects individually before reattaching them.
Now I can export to unreal and everything works correctly. If you want to be sure that your imported character is properly scaled. Attach a socket the root bone in unreal and attach the original mannequin to that socket. The two characters should overlap, if one is towering over the other then there is a problem.