Keef,
I think what you'll need to do is to model the parts you want to be offset in a layer on their own (in the un-rotated/offset position). Then you can apply a morph to them to place them in the final position.
That way, when loading into Layout, simply attach morphmixer and crank the appropriate morph channel up to 100% - you should then have a correctly displaced object that moves with the correct orientations.
Alternatively, you could also try rotating the pivot point of the layer to the correct offset - this might also work...
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