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Ethernets do not suffer a 20% loss in efficiency due to 8/10 coding as implementation loss is counted from the 1Gbps bit rate, not the 1.25Gbps line rate.
I also think your calculation for burst overhead is severe, and not in line with the 1micro-second guard band that is being promoted.
Overall I would say that upstream efficiency can easily be higher than 80% (and not the 50% presented).
I would also like to isolate upstream efficiency induced by link limitations, such as laser performance, from MPCP efficiency.
I believe there is no penalty associated with the proposed protocol, that is in line with Ethernet in general. Upstream utilization will be maximized based on the performance of the optics.