As a woman with a chronic health condition, this conclusion seems like it was reached by those who are generally considered healthy. Some of the most common dietary changes for people who suffer from a chronic health condition are to increase your vitamin D and B12 intake, and to consider a higher protein/low sugar diet. Especially since this study looked at multimorbidity, I think the Occam's razor argument would be: get diagnosis 1, make recommended dietary changes given to you by your doctor, get diagnosis 2 because these conditions tend to run in packs.

This was a good idea for something to study, but I wish it had been presented as "here are things that are highly correlated" rather than "this is caused by X", because it shows a blind spot from either the researchers or the writer.