USB termination on STM32F437xx
The reason hardware designers put the extra pads in is because they live in the real world. Chip manufacturers often claim a lot of things, especially in their 'preliminary datasheets' (power consumption figures are notoriously bad) only to drop the ball on production parts. This can be particularly important for things such as high speed termination resistors, where a wrong value can cause signal or EMC issues that you'll only discover on a finished board. Having the pads there means the hardware engineer can easily add some extra resistance if they find the design is not performing as required.

For example, the early STM32 parts were advertised as having built-in 1.5kΩ pull-up resistors on the USB lines. This was a great feature, except that it turned out all production units only had 0.81kΩ to 0.95kΩ resistors due to manufacturing issues. This would not allow a device to pass USB compliance and needed quite an extensive redesign to fix the issue.

A few extra pads and jumpers isn't really worth much compared to the costs of having to re-do a board near the end of the design cycle and this is why good hardware designers will act very conservatively on these sorts of things until they have experience that the chip manufacturer is delivering on their promises.