First - you are talking two completely different systems. The hot start lever is a cable activated plunger on the carb that allows air in the primary circuit to start a bike in a flooded condition. The auto decomp is for starting the bike by opening the exhaust valves slightly to ease the compression on initial rollover.
I do not see why you could not eliminate the auto decomp system but why would you ? It is there for a reason and set up properly they work
If you inspected it twice I take it that you checked the gap setting and verified it is correct? - it is working as it should ?
"It's all about motorbikes - Always has been, always will be"