Sure, but when traffic jams happen you often see not just ONE lane of traffic slowing down at the merge point but ALL lanes of traffic slowing down. On a four lane freeway narrowing to three lanes it's not the case that the two right lanes are stop & go and the two left lanes are 80MPH. EVERYONE slows to 10MPH. Furthermore the notion that you'll get 2000 cars per hour at the merge point irrespective of speed is ludicrous. Once everything slows down people act really douchey and don't let each other merge, etc.
I have witnessed eight lanes of traffic slow from 70MPH to 10MPH over a single poorly designed merge when there was more than enough aggregate free space for the merge. That happened because drivers don't accelerate hard enough on onramps and people don't redistribute themselves prior to shitty merges.
Show me a society that has no traffic jams and I'll show you one that's ready for socialism. Or vice versa.
It's not about velocity it's about rate of cars through a point per hour. If you have a mergepoint with 10 lanes. Each lane can support say 20 cars per minute. If you have 200 cars approaching the merge-point per minute the cars can travel effectively at the speed of their choice.
If you close one lane, reducing the capacity of the mergepoint to 180 cars per minute while 200 cars are approaching a queue will build. The speed with which the cars mass the mergepoint is not relevant because the rate of cars per lane per minute will stay basically at 20 cars/lane/min.
As to your point about all lanes slowing down - cars will always redistribute as you can imagine. People tend to merge left as there's an additional traffic stream merging on their right. The writer made points about the capacity of the mergepoint vs. the cars approaching- not individual lanes and speeds.
In the context of the article your first point is the key question. The author argues that the flow rate is relatively constant even with varying speed. I would tend to agree that it would be fairly constant but if there was extremely efficient merging I could see the flow rate increasing by a few percent. Theoretically the difference in flow rate if cars maintain a 2 second delay from the previous car should be the difference in the length of time that it takes the actual length of the car to pass through the merge point.
So if the car is travelling at .5 carlengths per second then the duration per car should be 4 seconds whereas if the car was travelling at 10 carlengths per second the duration per car should be only 2.1 seconds.