I believe not having periods for the time you state usually does mean menopause. It is possible to continue to have endo & endo symptoms post-menopause though menopause for a lot of women means lesions can stop being stimulated that's not the case for all women. (My endo specialist told me that - I'm 45).
If it were me, and your direct experience says one thing but your doc says your organs say something else, I'd ask for an endocrine screening to check the levels of my sex hormones. Easiest way to see if you are in menopause is to see where your oestrogen levels are by scientific measurement! That should confirm it one way or the other.
I have experienced some peri-menopausal symptoms caused by endometriomas. I think they affect ovulation and so I believe now, lack of ovulation affected my progesterone levels, putting me in the hormone balance you see with perimenopause - the first stage where progesterone drops but oestrogen is still up. That can kick insomnia, night sweats, anxiety, all sorts! It takes oestrogen longer to drop for you to then enter cessation of periods. (This is all my logic based on my own experience after 42). Once I had my ovary cleared, those symptoms vanished. (They have since come back, along with another endometrioma so I'm definitely seeing a pattern here for me).
My periods haven't stopped though, which means oestrogen is still around, even on progestogen tabs, which I'm on to slow the endo down.
I'd get your hormone levels checked to find out what is happening. Treatment choices will vary depending on which side of menopause you're on, so it sounds pretty important this is confirmed one way or another. Good luck!

I get symptoms of starting a period but nothing comes down. Just a little blood on the toilet paper and bloody tissues in the bowl. But I am on Depo Provera. So mine is most likely stopped by that.