The company gives you the chance to submit the investment proofs, so that they can deduct your TDS accordingly ( i.e. after considering the claims the TDS will get reduced).
If you miss that chance then the TDS gets deducted at higher rate. Although you can claim your investment proofs at the time of filing your return, and claim refund of the tax which you paid excess earlier.
In a nutshell the company gives you a chance to get lower TDS deducted, so no need to wait for refund. Else you can claim the same with the income tax department and get the refund post processing your refund.