Alternative approaches...
Sorry to everyone who suggested that a Nazi or ISIS flag would be permitted, if you read the guide, the only military flags that don't need consent are, "Any flag of Her Majesty’s forces;". Those who suggested claiming it was a House flag, that must be "the name, emblem, device or trademark of the company (or person) occupying the building".
So, he could avoid asking for consent by:
1) Applying to Her Majesty for a Letter of marque, making him a privateer, i.e., leagalised pirate.
or
2) Registering a company, and making the flag the trademark of the company
or
3) Asking the College of Arms to grant a new Coat of Arms or Badge
Frankly, planning permission seems like the cheapest and easiest option, followed by (2). Elizabeth II doesn't seem to agree with Elizabeth I on the subject of privateers.