Disclaimer: Not a doctor, this is what I've learned from a being around vocal performers for most of my life.

Whispering is a surprisingly "high stress" activity for your larynx. When most people whisper they're not just pushing a little air past their vocal folds, they're tightening their vocal folds so much that they can't vibrate and produce the sounds your normal speaking voice produces. That's very tough on your vocal folds and trachea, and can cause or worsen laryngitis and tracheal strain. Whispering a lot is one of the behaviours that singers and ENT doctors might call "vocal cord abuse" and you shouldn't do it - your normal speaking voice is the safest and least stressful option if you want to speak.

You should definitely have a long, mature, sober think about how you're expressing yourself - vocal cord damage can become permanent if it's not taken seriously.

Your vocal tract and trachea are both also very important for swallowing. It's possible what your doctor is saying is that you have irritated, strained, or caused swelling in your larynx or trachea, and that issue is interfering with your ability to swallow fully.

If you're concerned or unsure please get your doctor's professional opinion. This is not a matter to trust to Reddit comments.

I’m also not a doctor but I am studying to become a speech-language pathologist and this is also the answer I would have given

I developed a habit of whispering my thoughts out loud. Do most people whisper their thoughts out loud or just speak in a regular pitch?

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Most people don't say their thoughts out loud at all. Of the minority who do talk to themselves, I'm sure very few have a habit of whispering.

So what do you do personally when no one is around.. do you whisper or not?

I might occasionally say something to myself but if I do so I will tend to use the same voice that I would use with others - for example if I have made a silly mistake I might grumble an expletive, or I might use a joyous tone if something is funny. I do not think I ever whisper to myself.

For the most part, however, my thoughts stay in my head.