I think it's because they noticed that most people want to pick up HYT1 at the end of khitomer (being able to fire two torpedos is nice when you're in the starter ship). The other two are sort of weak BOs anyway, since you cannot do too much with them until you get to the next ship.
Frankly, I've always found that photons fire two on their own often enough that the minor improvement of THY1 doesn't really do much. Tachyon Beam 1 actually seems to do something on those early ships, and it's never too soon to have a healer on the ground
But I think the issue really is why take away the choice? It wasn't hurting anything. It couldn't, as the very next mission gives you another BOff.
I want my future alts to be able to pick up that Vulcan cutie, not to mention. >.>