MaterialUIScaler ended up being the culprit for the InputField layout (and some other) issues.
I've modified the way it gets the scaling factor from CanvasScaler to be more reliable (ie: actually work), so the InputField layout issue when scaled should be gone in the next version (v1.1.6).
As the Asset Store approval process can sometimes take a while, I've also made a small patch package for v1.1.5, that changes the files necessary to fix the issue. If you'd like a copy, email us (email@example.com) and we'll send you one.
Sincerest apologies for any inconveniences due to the time it took to fix this.