It started sometime in the 50's, and to my knowledge is only found on the bottom side of Hesalite crystals.
Don't know if Omega aligned it a certain way, but I've seen them all sorts of angles. Might have been replaced differently during a service though.
The crystals are round so can be installed in any degree of rotation. If you have a really fussy watchmaker, they may take the trouble to align it to the face of the watch. Mostly it's just pot luck if it is like that.
I am so glad I found this! I noticed it on my new Speedy Pro and immediately panicked that I scratched the hesalite. I was about to jump on a train and take it back as I have been so careful, knowing that hesalite is quite easy to scratch. I couldn't understand why the surface seemed flawless - now I do!! Mind you, I can't really make it out as the Omega symbol, it's pretty damn small! Now I can relax and enjoy it!