[Bug] Missing Configuration in bookkeeper.conf

### Search before asking

- [X] I searched in the [issues](https://github.com/apache/pulsar/issues) and found nothing similar.

### Read release policy

- [X] I understand that unsupported versions don't get bug fixes. I will attempt to reproduce the issue on a supported version of Pulsar client and Pulsar broker.

### Version

OS - macOS 14.5 (23F79)
Java Version - 17
Pulsar Client Version - 4.0.1, 3.0.x
Pulsar Broker Version - 4.0.1, 3.0.x

### Minimal reproduce step

- Set env values for `minorCompactionMaxTimeMillis` and `majorCompactionMaxTimeMillis` and run `apply-config-from-env.py`.

Alternatively, it can be reproduced using pulsar-helm-chart and populating the values in `.Values.bookkeeper.configData`. Internally it uses the `apply-config-from-env.py` script to update values in `bookkeeper.conf`.

### What did you expect to see?

`minorCompactionMaxTimeMillis` and `majorCompactionMaxTimeMillis` parameters being configured in bookkeeper.conf.

### What did you see instead?

`minorCompactionMaxTimeMillis` and `majorCompactionMaxTimeMillis` parameters are missing from bookkeeper.conf even after running the script.

### Anything else?

We need to add these parameters to `bookkeeper.conf` to allow the script to update them.

### Are you willing to submit a PR?

- [X] I'm willing to submit a PR!

Locate bookkeeper.conf and apply-config-from-env.py, then compare the named settings with existing configuration entries. Reproduce using the two environment variables or pulsar-helm-chart's .Values.bookkeeper.configData; done when both parameters appear in bookkeeper.conf after the script runs.

Written by the indexing model from the issue text.