While not perfect the ai helps
* **Incomplete exhaust:**
I think the ai text is stating that the port at bdc must take away from the total stroke. If it's open at the last 1% then that engine is only 99% as efficient as one that doesn't have a port.
Also that port stops the scavenging effect of the valved exhaust. Although perhaps that could be mitigated by routing both to a common exhaust pipe.
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* **Fresh air loss:**
Indeed it was clumsy on its wording for the intake stroke. Basically on the bdc of the intake/compression stroke some of the intake charge will be lost to the open exhaust port.