When designing graphics to be super imposed in editing or live video situations, I make use of dummy footage, which I define as Guide Layer, to prevent them from being included in the final renders, where there should be alpha in stead of the dummy footage.
Unfortunately, this Guide Layer is included when using the T switch (Preserve underlying Transparency), which makes it a lot harder to achieve some effects, such as combining Alpha and Luma matting.
Please let Ae ignore the Guide Layers always, also in the compositing - guides should have no effect at all.