1. Is the inclusion of WTC relevant to the Kane reference, or is it just there to be juxtaposed with the cemetery and its connotations?
2. What's the significance of the fact that Snyder's shot is the reverse of Kane's? Is he contrasting the characters (whether just Kane and Blake, or their respective "mourning", or maybe even SAK and the weeping angel), or did the way it's presented in the comic necessitate that direction?
1. My guess is that Snyder decided that Blake's funeral clearly wasn't on Manhattan island, and it looks like New Jersey to me. Not sure as to why the WTC was in the background, but I liked it.
2. I think Snyder was just paying another homage, but without people realizing it.
Tracking shots like this exist in any films, I don't think Snyder was intentionally paying homage to that shot in Citizen Kane.
The funeral may well have been on Manhattan, what we're seeing here is the burial. I've been to many funerals that take place at a church, then, everyone gets into their cars, follows the hearse to the cemetery and then finished up with a service by the plot. There are no public cemeteries taking new "customers" on Manhattan island.
The WTC appears in the background in many shots and was intentional. The filmmakers wanted to continue to remind the audience that these events were not happening in the present day.