Yes, sending the object to layout (or synchronising) will send the entire object (ie: all layers within that current object).
You'll need to either: (a) delete the object layers you don't need in layout or (b) go into the layer browser in modeller, and set the visible flag (the last column - the one with the header that looks like an eye) to off (just click in it and the little dot should disappear) - this will stop the layer being loaded into layout.
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