I don't see how that's the case. What is "50% bigger"? I understand it as 150% of the size. Similarly, I would understand "90% bigger" to mean "190% of the size" and "100% bigger" to mean "200% of the size", and I'm sure that is how they are used in practice.
So then surely "200% bigger" means "300% of the size"? And "two times bigger" - which is mathematically identical to "200% bigger" - would be three times the size. I acknowledge that the phrase is often used like you say but I don't think that is its literal meaning, and if you used that in a contract I think it would legally be interpretted in the way I've said (I'm thinking of consumer law in a situation where something is "n times bigger for the same price").
All this applies analagously to speed and x times faster. I gave the examples above with size because I think it's a bit more of a common thing to talk about this way and speed is a bit more subtle because what we're measuring here is the time which is something / "speed" and here the numerator isn't clear (number of training runs perhaps).