### What this PR does / why we need it?
The pad `-1` modification is from
https://github.com/vllm-project/vllm/pull/25743.
It still has bugs for batched chunked prefill.
- vLLM version: v0.12.0
- vLLM main:
ad32e3e19c
Signed-off-by: drslark <slarksblood@qq.com>
Co-authored-by: Mengqing Cao <cmq0113@163.com>