Upon looking into it further, this just seems to be an issue with the ordering of SOURCE_INFO elements in source_sync.sh.
Specifically, since nv-tegra.nvidia.com/kernel/nvethernetrm.git is cloned prior to nv-tegra.nvidia.com/linux-nvidia.git, git obviously refuses to clone linux-nvidia into a non-empty directory. The easiest solution is to just patch source_sync.sh such that linux-nvidia.git is cloned prior to the other repositories that will be entailed within it:
@@ -59,9 +59,9 @@ SCRIPT_NAME=`basename $0`
# NOTE: *Add only kernel repos here. Add new repos separately below. Keep related repos together*
SOURCE_INFO="
k:kernel/kernel-5.10:nv-tegra.nvidia.com/linux-5.10.git:
-k:kernel/nvidia/drivers/net/ethernet/nvidia/nvethernet/nvethernetrm:nv-tegra.nvidia.com/kernel/nvethernetrm.git:
k:kernel/nvgpu:nv-tegra.nvidia.com/linux-nvgpu.git:
k:kernel/nvidia:nv-tegra.nvidia.com/linux-nvidia.git:
+k:kernel/nvidia/drivers/net/ethernet/nvidia/nvethernet/nvethernetrm:nv-tegra.nvidia.com/kernel/nvethernetrm.git:
k:hardware/nvidia/platform/tegra/common:nv-tegra.nvidia.com/device/hardware/nvidia/platform/tegra/common.git:
k:hardware/nvidia/soc/t19x:nv-tegra.nvidia.com/device/hardware/nvidia/soc/t19x.git:
k:hardware/nvidia/platform/t19x/common:nv-tegra.nvidia.com/device/hardware/nvidia/platform/t19x/common.git:
Alternatively, cd into nvidia directory, then:
git init
git remote add origin git://nv-tegra.nvidia.com/linux-nvidia.git
git fetch --depth=1 origin jetson_35.1
git checkout FETCH_HEAD