[Requiem]

The flagships all have a rectangular 'flag' above the masts to identify them from the other ships.
They are disabled the same way as sinking a normal ship, just do not use firebrand or they will sink.
If you have disabled one, and have been given the green circles to grapple on to, then you have done it correctly.
If you cannot board, I am unaware of any limitations to boarding a ship while on basic access. You may want to send in a bug report on that.