I just bought a MFT3 and read this thread and freaked out based on the comments that you have to readjust square everytime you change material thickness. I ran out to the garage and started looking more closely at my table. Turns out the OP is correct, you can skew but support by raising and lowering it but it's the result of user error.
So, the problem technically exists but only if you aren't following the proper steps to adjust the rail height. Bohdan and Jamanjeval are correct in their approach. When you raise and lower the guides you have to have the rail down, on top of the material being cut and also atop of the front support. The pin needs to be in the T-track and the support arms to the left and right need to be in contact with the rail (push up on the support from the bottom). When you do this you're basically squaring the support bracket to the rail, which is parallel to the table and tracks but also perpendicular to the plastic piece that the metal support rides over. When you clamp everything down after pressing the support up into the guide rail it's self squaring. If you don't apply pressure from the bottom up you risk there being a gap on either the left or right fence support 'arms' on the bracket, which results in a skewed bracket and out of square cut.
All that being said, it could be designed better and the more I look at the entire assembly the cheaper it looks to me.
Hope that helps!