Under the Pension Act, pensioners who are assessed at 100% disability and who have exceptional care needs are eligible to receive the exceptional incapacity allowance. That's under the pension legislation.
Under the new Veterans Charter, another allowance was created called a permanent impairment allowance, which is somewhat similar but not completely analogous to the old exceptional incapacity allowance.
All this provision is saying is that you can't qualify to receive both the exceptional incapacity allowance under the Pension Act and the permanent impairment allowance under the new Veterans Charter. It is simply stating very clearly that if your benefits accrue under the old act, that's where you will receive them. If they accrue under the new act, you will receive compensation under the new Veterans Charter.