There is no contradiction between the two documents:
– the schematic shows the index of the pin on the corresponding pin headers. Due to the layout of the mapped out pins, the entire P9 is split into three sections, therefore the pin number restarts from 1 on the SYS_5V pins.
– the online manual shows the actual logic name of the pin, and is the only thing that matters to you when writing software.
The 33Kohm resistor is used to protect the rain sensor GPIO in case someone accidentally connected 24V AC to the rain sensor port (believe it or not, this happened in the past!). 33K, 30K, 27K all work fine, depending on what resistors we have in stock.