Personally I don't think it's a massive risk to the lower back.
The greater concern in my opinion is the transfer of power from the hamstrings. At the bottom what should happen is the lower back remain solid which provides stretch to the hamstrings and forces them to contract hard with the stretch reflex.
If you lose tension at that point, the transfer of power from the hamstrings is lost making the movement less efficient and lowers the contribution of the hamstrings. For me that's the bigger worry, it can lead to other problems down the road.
So yes, continue to stretch all relevant areas and work toward less winking.