None of this is certain
This is a statistical study, so it's not meant to be. Nobody in the field expects it to be because it's measuring relative risk to guide decisions.
none of this was precise
Yes, it was. Parameters were constrained to realize the statistical comparison of the sample, as it's standard practice. Also note the huge sample size that only adds to its precision by reducing the margin of error.
scientists primarily focus on our diets - our eating frequency, activity levels, digestion, metabolism
This is what the article is doing, but in the context of a behavior-altering substance like cannabis.
demonizing cannabis unfairly.
No part of the article does that. If you're only reading clickbait titles, you're doing it wrong. Quite the contrary, it's fully transparent and reasonable in its purpose.
There is no mechanism or pathway the authors have proven exists that cannabis or a particular cannabinoid damages the endocrine system/etc. by itself
No part of the article suggests that, and directly states the possible explanation is a change in eating habits.