Why are personal and employer pensions separate in the self-assessment

If I'm understanding correctly, personal pension contributions (SIPP) go into the first box (Payments to registered pension schemes), while contributions to employer pensions which don't take contributions before tax go into a later box (Payments to your employer's scheme). My question is why are these separate boxes in the first place? From a tax perspective isn't it all operating the same way, with the pension provider providing relief at source? Or am I completely misunderstanding the question here?

Hi alwaysconfused,
This is to ensure that it is identified who is makling the payment and the type of pension scheme.
Thank you. 

The notes that go with the tax return - https://www.gov.uk/government/publications/self-assessment-tax-return-sa100 - explain that the "Payments to your employer's scheme" is only for schemes where you paid in and relief at source was NOT applied.

Hi I'm not a HMRC Admin, but are you talking about the notes for box 3? If so box 3 is for payments you make to an under net pay scheme (which are deducted before tax) where you made the payment from your net pay instead of your employer deducting and paying it (as is normally the case with under net pay schemes). There needs to be distinction because relief at source schemes, the pension will claim the 20% basic rate relief and the remainder will be relieved by extending your basic rate band. This is box 1. While those made from net pay to a under net pay scheme will not have any relief claimed by the pension so need to be dealt with differently. Which is why there needs to be multiple boxes on the return.