The problem with this subject is that there's a LOT of female sex steroids and a lot of HRT drugs.
People tend to talk about HRT like it's all one thing but it's not.
Ethylestradiol used in birth control pill and some HRT supplements has probably the most risks of cardiovascular health.
Regular estradiol based HRT you have to keep in mind many of the studies have been done with women taking it and increasing exposure well beyond a normal timeframe, and thus might not apply to us.
There's issues with Progesterone but most of those studies involve Medroxyprogesterone, chemically different. As opposed to the compound naturally found in the human body.
As someone mentioned pregnancy has a habit of reducing autoimmune symptoms, most of the research on that implicates Estriol, which most TS's don't take anyway, in having that effect.
Let me put it this way, I used to get sick a lot, since I started HRT I've gotten sick less. Might be totally unrelated, but that's the thing. If there are effects they're minor.
Personally I wouldn't worry about the studies, because you need to understand the full picture to take anything from it, and if you do all you can usually take from it is a whole bunch of 'maybe's.