This is a pretty counter-intuitive game mechanic, but pretty much everyone learns about it if they are trying to get better. It's one of those "spend apm, gain a slight advantage" kind of things which i dont really love as it doesn't add anything to the game strategy-wise, but just forces higher apm to maximize your play. I don't really mind it either though, and don't think there is much of a good solution without changing game mechanics significantly. However, just reducing the upgrade cost vs the straight build cost for mexes I wouldn't mind either.
One thing that REALLY DOES bug me, is the time for the animation of the mex ctrl-k that you have to wait for before you can place the t3 mex order. Can we speed that up? It's only like 2 seconds or something, but then when the game is lagging it feels like i'm wasting A LOT of time staring at my mex waiting to be able to give the build order, but it's not long enough to justify looking away and doing something else.