The impression I've gained is that way more of us have hormone-related problems than is the case for the cis population, which is one reason for thinking that transness is a kind of intersex condition. I myself have congenital secondary hypogonadism, which had worsened to the point where I was experiencing a lot of health problems due to low T prior to starting on hormones. I certainly feel much better now than I did then, and the last time I had my blood work done, everything looked OK too.
If you've got existing hormonal problems then your body clearly isn't doing a very good job of managing things on its own, so I'd have thought that (provided it's done correctly), HRT should, if anything, help to improve the situation!