You will find with the correct slack the chain will contact the underside of the swingarm with not weight on the wheel.
The best way is, as mentioned, to get a baseline setting with the linkage bones disconnected and axle in line with output shaft. You only have to do this once.
Prop the back wheel in that position and set the chain to about 5mm slack. Connect the linkage bones back up and now measure, or get a 'feel' for, the slack in which ever position you normally adjust your chain (on side stand, centre stand, paddock stand etc.) Make a note of this slack as a reference point for future adjustments.
Also remember a 'hot' chain after a ride will always be slightly looser than a cold one.
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