It makes absolutely no difference at year end because HMRC tot up your earnings from all sources, deduct your personal allowance coding then charge you income tax at the appropriate bands on the whole earnings. They then compare to what's been deducted by the employers. If you've paid too much you get a refund and vice versa.
The logic and what you are going currently works because your first job does not pay enough to hit the tax threshold, and the general ruling is that HMRC get the second employee to deduct tax at Basic Rate (20%) using a 'BR' coding. Most people's first job (of several) usually pays enough to put them into a tax paying bracket so charging the second job at Basic Rate tax is correct for many people.