There is a significant difference between a bond and paying for your training.
If it is a bond, you do not pay anything for your training so there is no tax relief. flybe operate this system.
If you pay for an aircraft rating before you join a company, forget any chance of tax relief. You trained off your own back and that was your decision. This applies to Ryanair pilots.
If however you train whilst employed by the company (bmi) the most cost effective way of reducing your tax liability (and your companies) is by salary sacrifice. Many companies employ this policy for pension contributions as it benefits everybody except the tax man.
There are 2 rules that you must satisfy to reduce your tax liability if you have paid personally for your rating. (As long as your employed by a company)
1) The employee is obliged to incur and pay as holder of the employment.
2) The amount is incurred wholly, exclusively and necessarily in the performance of the duties of the employment.
If you can satisfy both conditions there is no problem in reducing your liability.
You will find that any sticking point will be in the wording of your employment contract.
Balpa are actively in talks with the IR to standardise the system. At the moment all cases are dealt with on an individual basis.