CLKIN1/CLKIN2 is for test purpose, if you need set the frequency for enet_timer2_clk_root, you just need to choose the source from ROOT88 you already know it, then set the corresponding pll frequency, you can refer to the dts file
linux-imx/arch/arm64/boot/dts/freescale/imx93.dtsi at lf-6.6.y · nxp-imx/linux-imx
clocks = <&clk IMX93_CLK_ENET1_GATE>,
<&clk IMX93_CLK_ENET1_GATE>,
<&clk IMX93_CLK_ENET_TIMER1>,
<&clk IMX93_CLK_ENET_REF>,
<&clk IMX93_CLK_ENET_REF_PHY>;
clock-names = "ipg", "ahb", "ptp",
"enet_clk_ref", "enet_out";
assigned-clocks = <&clk IMX93_CLK_ENET_TIMER1>,
<&clk IMX93_CLK_ENET_REF>,
<&clk IMX93_CLK_ENET_REF_PHY>;
assigned-clock-parents = <&clk IMX93_CLK_SYS_PLL_PFD1_DIV2>,
<&clk IMX93_CLK_SYS_PLL_PFD0_DIV2>,
<&clk IMX93_CLK_SYS_PLL_PFD1_DIV2>;
assigned-clock-rates = <100000000>, <250000000>, <50000000>;