Fitter doesn't assign HPS DDR3 pins

First thing is that you had look into the wrong table, you should look into the table 11 U670 device, which only have 145 IO

second is that you have HPS inout pin that is not connected to the module, Quartus will not able to identify those pin are HPS thus it will assume it as the GPIO. This will cause it have more GPIO pin.

// inout HPS_I2C0_SCLK,

// inout HPS_I2C0_SDAT,

// inout HPS_I2C1_SCLK,

// inout HPS_I2C1_SDAT,

// inout HPS_KEY,

// inout HPS_LED,

// inout HPS_LTC_GPIO,

// output HPS_SD_CLK,

// inout HPS_SD_CMD,

// inout [3:0] HPS_SD_DATA,

// output HPS_SPIM_CLK,

// input HPS_SPIM_MISO,

// output HPS_SPIM_MOSI,

// inout HPS_SPIM_SS,