Hello @XD,
Thanks for the detailed description of your problem. My understanding is that you want to achieve the following configuration [page 2760, S32G3 Reference Manual, Rev. 4, 02/2024]:


Which will output GMAC0, PFE_EMAC0 and PFE_EMAC1.
As you mentioned, the table 7 in the BSP41 manual only mentions Serdes 1 in mode 1, this might be an error in the documentation, Since in the next subsection 7.2.2.1 Example configurations [page 50 and 51, Linux BSP 41.0 User Manual for S32G3 platforms] you can see mode one is also configured for SerDes 0:

I will have to confirm with the internal team if it is an error.
and you can also see SerDes 1 in mode 3:

Following these two examples the correct configuration is:
serdes0:mode=pcie&xpcs0,clock=ext,fmhz=100;pcie0:mode=rc;xpcs0_0:speed=1G,an=0;serdes1:mode=xpcs0&xpcs1,clock=ext,fmhz=125;xpcs1_0:speed=1G,an=0;xpcs1_1:speed=1G
As you can see, with this configuration you get Serdes 0 (serdes@40480000) in mode 1 and Serdes 1 (serdes@44180000) in mode 3:
U-Boot 2022.04+g4744d0e2c8+p0 (May 27 2024 - 09:33:20 +0000)
SoC: NXP S32G399A rev. 1.1
CPU: ARM Cortex-A53 r0p4 @ max 1300 MHz
Model: NXP S32G399A-RDB3
DRAM: 3.5 GiB
Core: 306 devices, 25 uclasses, devicetree: board
MMC: FSL_SDHC: 0
Loading Environment from MMC... OK
s32cc_serdes_phy serdes@40480000: Using mode 1 for SerDes subsystem
s32cc_serdes_phy serdes@40480000: Unstable RX detected on XPCS0
pci_s32cc pcie@40400000: Configuring as RootComplex
pci_s32cc pcie@40400000: Failed to get link up
In: serial@401c8000
Out: serial@401c8000
Err: serial@401c8000
Board revision: RDB3 Revision F
PCIe: BusDevFun VendorId DeviceId Device Class Sub-Class
__________________________________________________________________________
pcie@40400000 RootComplex
| `-- 01:00.00 0x1957 0x4300 Bridge device 0x04
Net: eth0: ethernet@4033c000
Found PFE version 0x0101 (S32G3)
pfeng pfeng-base: Uploading CLASS firmware
pfeng pfeng-base: EMAC0 block was initialized
pfeng pfeng-base: EMAC1 block was initialized
pfeng pfeng-base: EMAC2 block was initialized
pfeng pfeng-base: Enabling the CLASS block
pfeng pfeng-base: PFE Platform started successfully (mask: 7)
s32cc_serdes_phy serdes@44180000: Using mode 3 for SerDes subsystem
s32cc_serdes_phy serdes@44180000: Unstable RX detected on XPCS1
s32cc_serdes_phy serdes@44180000: Unstable RX detected on XPCS0
, eth1: pfe0, eth2: pfe1, eth3: pfe2
Hit any key to stop autoboot: 0
=>
=> printenv hwconfig
hwconfig=serdes0:mode=pcie&xpcs0,clock=ext,fmhz=100;pcie0:mode=rc;xpcs0_0:speed=1G,an=0;serdes1:mode=xpcs0&xpcs1,clock=ext,fmhz=125;xpcs1_0:speed=1G,an=0;xpcs1_1:speed=1G
=> xpcs list
Registered XPCS instances:
| ID | SerDes instance | XPCS |
| 0 | serdes@40480000 | 0 |
| 1 | serdes@44180000 | 1 |
| 2 | serdes@44180000 | 0 |
=>
In the mentioned section you will also see how to configure the switch 17 and switch 8 to obtain the desired result in your RDB3.
For more details about the switches configuration you can check the RDB3 schematics [S32G-VNP-RDB3-DESIGN-FILES] in page 6:


As you are probably aware for this configuration you will need to reconfigure the SJA110, for which you need the SJA1110 SDK and it requires to sign an NDA. For this I can recommend contacting your FAE/DFAE/NXP representative so he/she may help you enabling this product in you account.
Let me know if this information solved your question.