appsettings.json

{
  "FromJsonValue":  "from json!"
}

NgProgram.cs

using ConsoleAppFramework;
using Microsoft.Extensions.Configuration;
using Microsoft.Extensions.DependencyInjection;
using Microsoft.Extensions.Options;

var app = ConsoleApp.Create()
    .ConfigureDefaultConfiguration(config =>
    {
        config.AddEnvironmentVariables();
    })
    .ConfigureServices((configuration, service) =>
    {
        service.Configure<HogeOptions>(configuration);
    });

app.Add("", ([FromServices] IOptions<HogeOptions> hoge) =>
{
    var a = hoge.Value.FromJsonValue; // ok
    var b = Environment.GetEnvironmentVariable("FromJsonValue"); // NG (null)
});

app.Run(args);

public class HogeOptions
{
    public string FromJsonValue { get; set; } = string.Empty;
}

OkProgram.cs

using ConsoleAppFramework;
using Microsoft.Extensions.Configuration;
using Microsoft.Extensions.DependencyInjection;
using Microsoft.Extensions.Options;

var app = ConsoleApp.Create()
    .ConfigureDefaultConfiguration(config =>
    {
        config.AddEnvironmentVariables();
    })
    .ConfigureServices((configuration, service) =>
    {
        foreach(var v in configuration.AsEnumerable())
        {
            Environment.SetEnvironmentVariable(v.Key, v.Value);
        }
        service.Configure<HogeOptions>(configuration);
    });

app.Add("", ([FromServices] IOptions<HogeOptions> hoge) =>
{
    var a = hoge.Value.FromJsonValue; // ok
    var b = Environment.GetEnvironmentVariable("FromJsonValue"); // ok
});

app.Run(args);

public class HogeOptions
{
    public string FromJsonValue { get; set; } = string.Empty;
}