What is the expected behaviour between the webjob app.config and the appservice web.config?
The expected behavior is that the WebJob will read the AppSettings from the AppService web.config, but for a custom configuration section, it will not read that configuration in the WebJob. If you want to read a custom configuration section in your WebJob, you will need to add it to the WebJob's app.config file.
I have created a console application in visual studio and then deployed in azure webjobs.

Iam able get the hello world output in webjob logs.

Then, I tried to add the custom configuration to the webjob app.config
as check below.
<configuration>
<appSettings>
<add key="MySetting" value="MyValue" />
</appSettings>
</configuration>
Added the below code in program.cs
and install Microsoft.Extensions.Configuration in your NuGet packages installer.
var configuration = new ConfigurationBuilder()
.AddJsonFile("appsettings.json", optional: true, reloadOnChange: true)
.Build();
var setting1 = configuration["Setting1"];
var setting2 = configuration["Setting2"];
Console.WriteLine($"Setting1 value: 123 {setting1}");
Console.WriteLine($"Setting2 value: 432 {setting2}");
Iam able run the app successfully in my local.

Then I re-deployed to the webjob and as expected am able run successfully.

Here are the logs.
