Resistor on SPI Chip Select Pin
would it be acceptable to use a resistor to decrease the voltage


I don't see any big problem with using a voltage divider for chip select.


  What would the upsides/downsides be of using an atmega running at 3.3v for the module with the MAX31865's 


At 3.3V you can only run at 13 MHz or less (so in practice, 8 MHz, unless you want to do a lot of fiddling around). This may or may not matter to you. At a lower voltage it uses less power which can be a plus, and you don't need to worry about level converters.


  and just using a hex converter on SDA/SCL for the I2C communication to the master?


Do you mean a level converter?