Hello @khan_misbah,
Thanks for the information, I compared the registers of my PFE1 using SGMII to your PFE2, I did not find much, however, what I did find are some differences in the Clause 45 registers, and following the BSP43 manual, section 7.3.1.1 GMAC U-Boot driver and checking the S32G2-EVB3 device tree for ATF/u-boot s32g2xxa-evb3.dts#L43 (and considering that GMAC and PFE interfaces have the same registers), can you try adding the following in &pfe_mdio2:
&pfe_mdio2 {
status = "okay";
/* TJA1104B */
pfe_mdio_b_phy2: ethernet-phy@2 {
compatible = "ethernet-phy-ieee802.3-c45";
reg = <27>;
};
};
You can also try configuring the CONFIG_PHY_NXP_C45_TJA11XX to your configuration with the menuconfig in u-boot:

Which adds support for the TJA11 family.
Since I do not have your board I cannot test the exact effects of the changes, however, please test each alone and then both.
If the problem persists, please also share the output of the dm tree command in u-boot, to compare it with my own.
By the way, I do understand that it is quite unusual that Linux works and u-boot does not, however, the device tree does not define the behavior of driver, it is only a descriptor, therefore Linux and u-boot have different behaviors.
Thanks in advance.