The fly commercial now to be more "eco-friendly".

Oh Iris how we miss ye

.... except when not flying commercial, scheduled common carriers.

At least some fly economy class sometimes too, even when there may be more than one class of service on board a plane.

As a practical matter, a booking can be made under names that don't match perfectly with the passports and still the passport information is acceptable for travel even to places with an APIS-type of requirement.

Some royals do, others don't. The RAF has a Royal Flight, but the biggest aircraft they're operating is a BAe-146s, which is far from the ideal choice traveling to Oz from UK. As such the UK royal family will either book commercial (paid by the country they visit if it's within the Commonwealth), or the visiting nation might send one of their aircraft if it's suitable for the task (like when Canada sends an A310 across the pond), of when Will and Kate went across the Tasman sea and the RNZAF made a 757 available. Again, it's the visited (Commonwealth) nation who foots the bill.

As for the '90 bags', perhaps QF charged overweight, though chances are that they didn't. And if they charged, it would be the Australian government picking up the tab.

No, they flew commercial because there wasn't any other option.

The Passport and Identity service has a detailed document on how passports can be embellished with observations on alternative names, titles and so on.

https://www.gov.uk/government/upload...-passports.pdf

But it seems unlikely that the Royal couple had to pass through formal immigration control.

They often pass through formal immigration control but it's usually handled by special liaisons from the receiving country and the sending country so that the wait in line in public view process doesn't take place. Sometimes they have to sit and wait in a special room or a vehicle for the immigration control formalities to be passed.

Prince William flew in economy coach a few weeks ago on American Airlines flight from Memphis to Dallas.

See here:

http://hollywoodlife.com/2014/05/06/...conomy-flight/

Queen & other Royals has been flying commercial for decades. They even use "ordinary" trains

Indeed. If you read the front of your passport it'll say:

"'Her Britannic Majesty's Secretary of State requests and requires in the name of Her Majesty all those whom it may concern to allow the bearer to pass freely without let or hindrance and to afford the bearer such assistance and protection as may be necessary.'"

So if Queen Elizabeth had a passport it'd be a bit like her singing the national anthem.

Also:

Correct me if I am wrong but isn't it the case that William and Charles cannot travel together due to their being 1st and 2nd in line to throne?

Wouldn't the same principle therefore prevent William and George travelling together?

No last name
 

Technically Prince William doesn't have a last name. Formally he would sign his name "William" with a line under it and the word "princepts." When modern society demands a last name,Royals have used various. Previously, they used WINDSOR. When Prince Charles was a helicopter pilot in the armed services, his personnel recordes identified him as Charles Wales. I think William and Harry use Wales because their dad did.

It serves as a basic form of data protection to avoid employees stumbling across it or searching for it with intent. Each company will have a policy/process for individuals of this level that travel - in fact there will be a database restricted to certain employees that holds the correct version (but not always).

In the US, the President does (apparently with the endorsement that "The Bearer is President of the United States" in case you didn't know), and even though passports are issued under the authority of the Secretary of State, he himself has one too.