I see where the confusion lies.
You are not really getting an advance on your Pay. You are getting an advance on your Travel Claim (or Travel Allowance).
You can do that. As your Claim will be processed, any money you are due will be put into your Pay. It is not really Pay per say, it is a Travel Allowance, and it is deposited in with your Pay once the Claim is 'Finalized'. Most people prefer not to take an Advance on a Travel Claim, because one often finds afterwards that they took too much and land up owing the Gov't money, and it is inturn deducted from your pay when the Claim is 'Finalized'.