What’s the reason for burraneer seniors and burraneer colts being different clubs? Are the colts aligned with their juniors?
In short: no, they are not aligned.
This is one of those classic cases of a Junior club having a Senior Arm who didn't see eye to eye. Remember, junior clubs operate under SJRU, while senior clubs operate under NSWSRU (Subbies), and therefore in most cases I'm aware of, they are separate entities from a legal and administrative point of view.
Without going into detail, sometimes there are differences of opinion that lead to antagonistic behaviour, and there is a split of some sort.
Burraneer Hammerheads - Subbies - exist because of such issues stemming from within Burraneer Dolphins - Juniors.
Georges River Rugby exists because of such issues stemming from within Oatley.
I'm not aware of anything particularly sordid, beyond disagreements that moved beyond the ability for all parties to come to a reasonable resolution.