It is not correct that sys3_pll_out use sys2_pll1_ref_sel as parent.
According to the current imx_clk_sccg_pll design, it uses both
bypass1/2, however set bypass2 as 1 is not correct, because it will
make sys[x]_pll_out use wrong parent and might access wrong registers.
So correct bypass2 to 0 and fix sys3_pll_out_sels.