soc: renesas: ra: Move configs from board deconfig into SoC deconfig

- Move config BUILD_OUTPUT_HEX and CLOK_CONTROL from board deconfig
into SoC deconfig
- Add clock-frequency in dts to get config
SYS_CLOCK_HW_CYCLES_PER_SEC from dts

Signed-off-by: Quy Tran <quy.tran.pz@renesas.com>