I am aware of the smog air at start up passages that are not used. Can it be used anyway?

 

Sure, why not? Honda blocked off the exhaust port in the intake manifold, so even that difference will not matter. The casting is the same as all other years.

 

As long as you don't want to use a stock PCM, no issue.

Stock PCM cars(00-05) can not run a 06 an later head without a CEL due to the missing air injection ports. MY06 and later cars won't care if injection ports are there or not.

It's not worth the machining hassle to add the injection ports and the port cover, far easier to find a early 00-05 head.