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I don't think it's possible. You're right, photos taken in LrM will sync back to one location on your Computer (that location can determined in LrD).
However, in LrM itself the best way to handle it probably would be to create a Collection and make sure you 'are in' that Collection when you use the LrM Camera. You can also Move other Photos to that Collection.
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You can choose a default collection where all your imported images will go (when using an other camera app).
But this doesn't apply to the pictures taken within the app, which is quite surprising.
It would make sense to be able to set a default collection for pictures taken with LR Camera.
(it may be possible, I just didn't find a way to do it)
It's surprising indeed!
Kind of encourages you to take pictures not with the LrM camera, but with another one and then import them to LrM :S
I hope they fix this in an update sometime soon..