If scripts are placed inside Plugins folder, they will be referenced twice in the C# Projects (Assembly-CSharp and Assembly-CSharp-firstpass) that is built for UWP or WSA. This will cause the following error:

Error CS0121 The call is ambiguous between the following methods or properties: [...]

This might have gone unnoticed before because the error is only a warning when dealing with normal classes, but when extensions are involved these become errors.

Reproducible in Unity 5.2.X and 5.3.

Forum thread:
http://forum.unity3d.com/threads/uwp-the-call-is-ambiguous-between-the-following-methods-or-properties-not-the-obvious-error.369049