That would be very unlikely, for the reasons outlined above. I would not say 'never', but I don't see any compelling reason, or any advantage it would bring. The only case I can think of is if you have already processed spritesheets but you don't have access to the original images, which raises other questions...
Looking at Cocos2d as an SDK example, I'll explain the assumptions I am making, and maybe you can tell me where I have it wrong and how packing textures
before using them in a level editor is useful.
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In Xcode, you can set up the texture packing as a pre-build step (
see the "To set up pre- or post-actions" section here), or as a separate target that is a dependency of your main project
as recommended by Texture Packer's developer. My assumption here was that one of these methods would be used.
Once this is set up you can edit the original images anytime, and every time you build your app the spritesheets will be automatically built without even needing to open the Texture Packer GUI itself. TP is also smart enough not to pack things again if nothing has changed, so it should not slow your build down.
In your app, sprites can either be loaded from a spritesheet (eg. createWithSpriteFrameName) or from an image file (eg. CCSprite::create). My assumption here was that the spritesheet would be tried first, then the image file as a fallback if the sprite frame cache did not contain the desired sprite.
You could change whether the original sprite gets used by clicking the checkbox in Xcode to include it in your main target or not, and you could change whether the sprite gets packed or not pretty easily by adding or removing it from the TP project. Obviously you need to have one or the other enabled to make the sprite available to your app

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As far as RUBE is concerned, all those steps are downstream in the tool chain so they make no difference. There is no need for the level creation step to be aware of any platform-related issues such as hardware accelerated texture decompression. For example let's say you go with .pvr.ccz files because they are a good choice for iPhone, then sometime in the future you want to release your game on a platform that does not support them... or suppose Apple comes up with an even better compression format and TP adds support for it. Changes like that should only have an effect on the final compiled app bundle, but if you're using the already processed spritesheets as part of your RUBE scene, the change would backwash all the way upstream to your level creation! Would you really want to maintain separate versions of your RUBE scenes to accomodate various platforms like that?
Well I think I have said enough

I have to admit I have not used TP for any projects myself yet, so let me know if there is something important that I'm not considering.