Just by comparing the default cfg that comes with Jetpack and the one created by a non-modified excel sheet the biggest difference I see is this is missing.
pinmux.0x02439054 = 0x00004400; # eqos_txc_pe0: eqos, tristate-disable, input-disable
pinmux.0x02439018 = 0x00004400; # eqos_td0_pe1: eqos, tristate-disable, input-disable
pinmux.0x02439010 = 0x00004400; # eqos_td1_pe2: eqos, tristate-disable, input-disable
pinmux.0x02439008 = 0x00004400; # eqos_td2_pe3: eqos, tristate-disable, input-disable
pinmux.0x02439000 = 0x00004400; # eqos_td3_pe4: eqos, tristate-disable, input-disable
pinmux.0x02439064 = 0x00004400; # eqos_tx_ctl_pe5: eqos, tristate-disable, input-disable
pinmux.0x02439040 = 0x00004450; # eqos_rd0_pe6: eqos, tristate-enable, input-enable
pinmux.0x02439030 = 0x00004450; # eqos_rd1_pe7: eqos, tristate-enable, input-enable
pinmux.0x02439028 = 0x00004450; # eqos_rd2_pf0: eqos, tristate-enable, input-enable
pinmux.0x02439020 = 0x00004450; # eqos_rd3_pf1: eqos, tristate-enable, input-enable, loopback-disable
pinmux.0x0243906c = 0x00000450; # eqos_rx_ctl_pf2: eqos, tristate-enable, input-enable
pinmux.0x0243905c = 0x00000450; # eqos_rxc_pf3: eqos, tristate-enable, input-enable
pinmux.0x02439038 = 0x00004448; # eqos_mdio_pf4: eqos, pull-up, tristate-disable, input-enable
pinmux.0x02439048 = 0x00004400; # eqos_mdc_pf5: eqos, tristate-disable, input-disable
Also SDMMC4 is missing
pinmux.0x02436004 = 0x00002460; # sdmmc4_clk: tristate-disable, input-enable
pinmux.0x02436008 = 0x00002448; # sdmmc4_cmd: pull-up, tristate-disable, input-enable
pinmux.0x0243602c = 0x00000448; # sdmmc4_dat0: pull-up, tristate-disable, input-enable
pinmux.0x02436028 = 0x00002448; # sdmmc4_dat1: pull-up, tristate-disable, input-enable
pinmux.0x02436024 = 0x00002448; # sdmmc4_dat2: pull-up, tristate-disable, input-enable
pinmux.0x02436020 = 0x00002448; # sdmmc4_dat3: pull-up, tristate-disable, input-enable
pinmux.0x0243601c = 0x00000448; # sdmmc4_dat4: pull-up, tristate-disable, input-enable
pinmux.0x02436018 = 0x00002448; # sdmmc4_dat5: pull-up, tristate-disable, input-enable
pinmux.0x02436014 = 0x00002448; # sdmmc4_dat6: pull-up, tristate-disable, input-enable
pinmux.0x02436010 = 0x00002448; # sdmmc4_dat7: pull-up, tristate-disable, input-enable
pinmux.0x0243600c = 0x00000450; # sdmmc4_dqs: tristate-enable, input-enable
And DirectDC1
pinmux.0x02435050 = 0x00022400; # directdc1_clk_pq0: directdc1, tristate-disable, input-disable
pinmux.0x02435048 = 0x00022454; # directdc1_in_pq1: directdc1, pull-down, tristate-enable, input-enable
pinmux.0x02435040 = 0x00022400; # directdc1_out0_pq2: directdc1, tristate-disable, input-disable
pinmux.0x02435038 = 0x00022400; # directdc1_out1_pq3: directdc1, tristate-disable, input-disable
pinmux.0x02435030 = 0x00022400; # directdc1_out2_pq4: directdc1, tristate-disable, input-disable
pinmux.0x02435028 = 0x00022400; # directdc1_out3_pq5: directdc1, tristate-disable, input-disable
and a few other misc changes
Hope this helps