Yes, onboard flash is on SPI bus, and SPI_CS 19 pin of C2 module (GPIO2/SPI_CS_0 B49 on AR9331) is the dedicated ChipSelect for it. You can use SPI bus pins for any other devices too, but You need a different ChipSelect pin! There are 2 additional hardware CS pin on AR9331: UART_RX 43 (GPIO9/UART_SIN/SPI_CS_1 B68) and UART_TX 44 (GPIO10/UART_SOUT/SPI_CS_2 A79) - GPIO / UART / SPI_CS function is muxed on these pins, You need to disable UART to reach another function. Or alternatively, You can use any other GPIO pin as ChipSelect - software CS gives a little bit higher cpuload and lower max speed, but its enough for most cases... But You need several modification in platform files!
RTC on SPI? It would be much easier to use an I2C based RTC like DS1307 on bitbanging I2C bus (kmod-i2c-gpio-custom)
Here it is a good article about MMC/SD card on hardware SPI bus:http://wiki.openwrt.org/ru/toh/tp-link/tl-mr3420/deep.mmc.hack
(google translate is Your friend!