Hi Aik,
now the changes are working as intended: a full reprogram (periph+core) of the FPGA is triggered on every reboot command by linux and also with the HPS cold reset button. Probably a more "elegant" solution would be an ifdef clause linked to a certain defconfig during the build stage of U-boot, in order to keep the compatibility with other boot sources (EPCQ/etc)...but it works.
About the double programming of peripherals, I've found some references in the official source code: https://github.com/altera-opensource/u-boot-socfpga/blob/61ae22e548ebda525d5216d107e45f20eca70537/arch/arm/mach-socfpga/misc_arria10.c#L142-L157
Could you please investigate internally with your colleagues if double periph config is needed on Arria 10 SoC?
Regards.