Take a look at the esp32s3 TRM chapter 6.3, table 6.2 and table 6.3 to understand relation between the IO MUX and the GPIO matrix.

IO MUX pin setting (selected function, drive strength, pull-up, pull-down, input enable) are controlled by the iomux: pinctrl@60009000 node, like this:

&iomux {
	spi2_pins: spi2_pins {
		pinctrl-single,pins = <
			PIN(9)  (FUN0_20MA)			/* CS1 */
			PIN(10) (FUN_SEL(4) | FUN_DRV_20MA)	/* CS0 */
			PIN(11) (FUN_SEL(4) | FUN_DRV_40MA)	/* MOSI */
			PIN(12) (FUN_SEL(4) | FUN_DRV_40MA)	/* SCK */
			PIN(13) (FUN_SEL(4) | FUN0_20MA_IE_WPU)>;/* MISO */
	};
};

These properties cannot be changed at runtime (short of writing directly to IO_MUX_n_REG registers).

When there's no direct connection for the function in the IO MUX or the pin with direct connection cannot be used a function may be routed through the GPIO matrix to a different GPIO and connected to a different pin. These settings are controlled by the nodes gpio_out_mux: gpio_out_mux@60004554 and gpio_in_mux: gpio_in_mux@60004154. Numbering schemes are different for output and input muxes. E.g. for the ouput mux a GPIO index is mapped to a peripheral signal (table 6.2):

&gpio_out_mux {
	spi2_gpio_out: spi2_gpio_out {
		pinctrl-single,pins = <
			GPIO_FUNC_OUT_SEL(9) 111>;		/* SPI2 CS1: GPIO9, signal 111 */
	};
};

For the input mux a peripheral signal is mapped to a GPIO index:

&gpio_in_mux {

	uart2_gpio_in: uart2_gpio_in {
		pinctrl-single,pins = <
			GPIO_FUNC_IN_SEL(18) 5>;		/* U2RXD: signal 18, GPIO5 */
	};
};

All used pinctrl phandles are then mentioned in the device's pinctrl property:

&spi2 {
	pinctrl-0 = <&spi2_pins &spi2_gpio_out>;
	pinctrl-names = "default";
};