Normally when flashing file layout is determined by the rootfs directory combined with some boot configuration edits. You could copy your customizations into the rootfs directory after the apply_binaries.sh step. By basing your rootfs on the R24.2 rootfs plus customization, flash will retain those changes (boot configuration may change, but regular user files in rootfs are copied verbatim, including your edits).
It might work to add the R24.2 root file system plus apply_binaries.sh, but this seems risky. I’d just flash the whole thing. There is no “upgrade” path to merge a living R24.1 into R24.2 (no patch). R24.2 is here: https://developer.nvidia.com/embedded/linux-tegra