Alpha is mostly slower when you actually alpha blend, if you do the alpha cutting or however the method is called in BFME it should just not render the parts that have alpha, though the edges won't be smooth 
But all this stuff really just depends on the engine and all that...
Also at a certain amount of vertices and all that the engine would simply crash due to you exceeding the amount of indices available 
Not entirely sure if they used shorts or integers or whatever, but depending on that... things could get interesting
To keep it simple though, as said before, optimize when possible, it's an amazing skill to have, one which some of my colleagues lack, which is actually quite annoying at times. Most of all, just test things out yourselves.
It's heavier to have a lot of different textures rather than more polygons, although this could also depend slightly on how the engine handles all this
