Why are these LED current limiting resistors so big?
The MCP73831 datasheet specifies a maximum source/sink current on the STAT pin of 35 mA and 25 mA respectively - so if the designer wanted brighter LEDs she could use lower-value resistors without worrying about overloading the output drivers on the charge controller IC. Higher currents would eat into the current available for charging, but not really to a significant extent.

So yes, I think the reason is simply that 6 mA is plenty bright enough for a status LED. Some would even say it's too bright, especially with modern high-efficiency LEDs.