Update the parser options with values from config file. Fixes #8447.

The way the parser merges the CLI configuration with the file configuration is.

For each option:

  1. If a value was passed to the CLI, that value rules.
  2. If not value was passed to the CLI and no value is defined in the config file. The default, it any, is used.
  3. If a value is not passed to the CLI and the value is defined in the config file, the config file one will be used.

Some code was using the parser options for logic and values after the configuration loaded, but the parser options were never updated to the configuration files values.
So:

  4. Do what we said in the above 3, **and**, update the parser option to have that value.
Merge pull request #9040 from s0undt3ch/issues/8447-timeout-from-configfile-not-respected

Update the parser options with values from config file. Fixes #8447.