It depends on the agreement with the local tax people. In the case of your friend, the Irish Revenue Commissioners do not tax allowances due to, I believe, an agreement with the civil service not to tax their allowances. Not out of altruism for pilots but the pen pushers in the civil service would throw fits if their allowances were taxed. Its something to do with the allowances being earned overseas and thus not taxable as only income earned within Ireland is taxable by the Irish authorities.
The situation is the same with other Irish carriers. The UK is different due to different agreements with the Inland Revenue.