SF was a given saying thats where Starfleet HQ is, as for other cities film producers tend to favour a few cities more than others, New York, London, Paris tend to be popular. Perhaps because they have more instant regonition to a worldwide audiance.
Which makes the helicopter scene a perfect place to plug in an unknown location. If the location was unrecognisable and looked foreign, with lots of Middle Eastern architecture, it would convey secrecy and caution, while contributing to location diversity well enough.
The meeting and Section 31 headquarters were the only two locations that weren't fixed by plot, circumstance and canon, the latter opportunity was utilised nicely showing us England, the former could have been used too.
Additional shots of departure of officers from multiple locations around the globe during the distress call in STXI would also work pretty well IMO, although it would be expensive probably?