Philly B, it might help if you read the thread before posting, because I explained what elements STiD borrows from Insurrection right before you posted. Both STI and STiD feature a rogue Starfleet Admiral with connections to Section 31 as an antagonist. They also share the common element/theme of the protagonists having to blatantly defy Starfleet rules and regs in order to defeat said rogue Admiral.
Xaios, I acknowledged that Dougherty's connections to Section 31 weren't mentioned/made clear in the film itself.
As to your second point, he might've had tacit permission to carry out the Ba'Ku relocation mission, but he was in fact acting as a rogue operative by actively keeping information from the Federation Council.