You're right, it shouldn't matter where we export from to the encoder (I only tried AE really... I was very pleased when I found color channel manipulation as an option there, no guide would even hint on it and they were all bsing about using transparent backgrounds for layers when composing no matter what word combinations I tried to feed Google). .webm is a very straightforward format, one of the reasons it is well liked. You do get some options you can tweak, yeah. I don't know if it's better/worse that the converter you linked because I am using a different one.