Current released real-time kernel package 4.9.201-rt134 tegra#1 doesn’t include CONFIG_HZ=1000. Is it possible to set it without recompile kernel? if no - do you plan to release version with CONFIG_HZ=1000?
CONFIG_HZ is not runtime-configurable, so you’ll have to recompile.
Rather ask your question in the Jetson forums:
This one is mostly about the x86 graphics driver, so hard to find someone who knows about the ARM platforms.