How do you size pull-up/down resistors?
As you have demonstrated with your experience pull-ups/downs generally can be a wide range of values and so if other parts of the design have used (say) a 57k6 for something more critical, why add another part to the bill-of-material - use what you already must have.

I'm not saying this is always going to be the case - I can imagine a scenario where a particular company may have excessive stock of one value - using that value helps the inventory.

As for the 2k2 resistors in series with the switches - your reasoning is good and it may also be that the switch is located some distance from the chip and the 2k2s protect the chip in some way. TDO is an output during JTAG programming - there isn't enough shown of the schematic to determine what the other line is.