SUMMARY
I am going to pile these up here because I think they're all symptoms of the same issue, namely the way how onion skins are composited.

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1. Grayscale animated layers have gray onion skins.
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STEPS TO REPRODUCE
1. Have an animated layer.
2. Show the onion skins, observe how colorful they are.
3. Convert the layer to grayscale.
4. Observe how onion skins are now gray.

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2. Transform tool boundary takes onion skins into account.
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1. Have an animated paint layer.
2. Try transforming a frame, observe the size of the bounding box.
3. Cancel transformation, turn on onion skins.
4. Try transforming the layer again, observe how the bounding box now is larger, large enough to encompass the frame and its onion skins.

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3. Onion skins can be color picked
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1. Have onion skins active on an animated layer.
2. Ctrl+click or whatever you have set 'pick color from merged image' to.
3. Observe you can pick colors from the onion skin.

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4. Onion skins affect the fill-tool results
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1. Have onion skins active on an animated layer.
2. Use the fill tool.
3. Observe how the onion skin is used by the fill tool as well.

Just to clarify, these are my fill tool settings:

Fast mode: No
Threshold: 0px
Grow selection: 1px
Feathering radius: 0px
Fill entire selection: No
Limit to current layer: No
Use pattern: No

I will add more as I come across them(and they seem to be an issue with compositing)