Why did you say "Arguably this does not require full sterilisation as it will not need to be shelf stable." The bigger the package, the more likely it is required to be shelf stable or shelf life will run out when the package is not empty.
You said: "But still needs to be safe for consumption and no chance for mould growth during the shelf life.
We do not want to fill hotter than 80degrees as the buckets become very flexible. "
How long is your cooling step?
Why are you using these flexible buckets? I would look for more thermo-stable buckets if I were in your position.