All the information you require on salary can be found
here.
You will notice that the difference between direct entry and cadet salary is £12k. That £12k is returned to the bank directly as your bond repayments, not via your salary, in £1k monthly instalments. It does not form part of your taxable salary, hence 'tax free'.
I would have thought that after earning £1000 a month for 6 months, that I would have effectively already paid for my TR, so would I then be entitled to a full salary?
Maybe/maybe not, however there is the small matter of your CPL/IR/MCC/AQC/ATPL theory to be paid back...