I was buying my first bike a few months ago, so my experience is fresh. Kinda from one noob to another one.

I would highly recommend LBS for the first bike. First, you learn what bike size you do need. Then, you can try as many bikes as you want and feel them. Buy the one you fell in love. ))) (and can afford)))))

The LBS will help you to fit the bike which is important too. Also, some of LBS will do some adjustments, services for free, and you need them.

The components are irrelevant until you know how much you actually will ride. From what you told, some commutes plus some longer rides, it is going to be 100-150 miles a week, correct? For this mileage, any components are fine. I wouldn't buy anything with thumb shifters, they are just not comfortable for any kind of ride. But the Sora on other components is fine.

I don't think components upgrade is very wise, because it can easily reach the half of the initial bike cost or more. Replace them only if they brake. Save it better for the next bike.

Don't forget to leave room in your budget for pedals, clothes, bottles, computer etc. It all adds up quickly.