Adam,
some very good points. However, flow bench testing of a header, and flow capability in general, has absolutely nothing to do with thermal dynamics or scavenging. Many people mis-understand scavenging for flow.
The Exhaust velocity can definitely be increased from simply using a true "merge collector" such as Burns Stainless offer. But, the difference in price to add just theis collector is $150.00. It's available if anyone wants it but in my opinion, it would be a huge waste of money on the shorty header. Maybe worth doing on the long tubes, but as you stated, the confines and limitations of the engine compartment dictate more in the design of the header than anything else. In other words, you wont feel the difference on the street.
In a nutshell, you want flow for the intake system and scavenging for the exhaust. Two totally different characteristics.
Got to run.