Why have resistors on a signal line
R3/C6 and R5/C7 form a low pass filter to remove stray RF etc. Having the pullup on the micro side would not have the same effect as with R2/R4. Sure, you could eliminate these components, but you might find nearby cell phones cause strange readings etc. You should always seek to limit the bandwidth of external signals.
The SPC_REG signal is open collector. I dare say the designer could've used the open collector feature of the micros port pins to do the same. The 10k resistor is needed to limit the base current for the transistor. It wouldn't like 5V being shoved where it only likes 0.7V