BostonB1

I am planning on leaving within this week. I am in the mid way of doing my USMLEs having passed two and preparing for the third and feel pretty bummed about this whole situation as my future is at stake. I am still grateful my extension was approved atleast till November and I am still within 180 day time frame. Let’s see what happens

Yeeeeah, this is where the US Extension of stay process really sucks. You're in authorized stay while your application is pending but that immediately turns to unlawful presence if that application is denied. I doubt USCIS would have granted you a second extension anyways, so regardless your time from November would've been unlawful presence on the balance of probabilities.
 
And yeah, you've gotta file extensions to cover the time you anticipate being in the country, so a pre-November filing would have been wise. That being said, you incur no inadmissibility so long as you depart prior to 180 days of unlawful presence. However, you'll have a higher burden to prove when you apply for a new B1/B2 visa that you won't overstay in the future. Consular Officers use 'reasonable person' determination based on the evidence presented to determine overstay risk when granting/denying visa applications. I would suggest you demonstrate very strong ties to your home country next time you apply for your visa. You should be thinking, hard documentary evidence of ties such as job, family, property in your home country.
 
You should depart as soon as possible to avoid incurring a 3 year bar having gained more than 180 days unlawful presence. Covid's been a thing for awhile and most countries have methods of returning, or you can go to any other country with lawful status, so the whole Covid excuse will only go so far with Consular Officers.

I realize that is how you interpreted the situation. I can’t say whether an interviewing officer might accept your misunderstanding as a valid reason. They usually don’t, to be frank, maybe you’ll get someone on a good day.

You've overstayed since November 2020.  Your visa is no longer valid because of the overstay.
 
The extension that you filed for is for 6 months.  That means the latest that extension would last is 6 months from May 30, 2020.  You didn't file to extend beyond those 6 months.
 
Rarely, does USCIS gets a response for an extension out within 6 months.  You can't blame USCIS delays for not leaving by November.
 
You need to leave the country as soon as possible.  You will have to apply for a new B1 visa.  At the visa interview, you will be given an opportunity to explain why you didn't leave at the end of the 6 month extension that you asked for.