Trans fat only occurs naturally in a few food sources, and at very low levels (Health Canada). If a food is high in trans fat, the trans fat there on purpose (e.g. processed foods use trans fats to improve texture, increase shelf life, etc.).
If a scientist's focus is saturated and unsaturated fat, and if food intake could be carefully controlled (such as in animal studies), they probably wouldn't include foods high in trans fat at all. For example, this study from 1990 compares soybean oil-based and lard-based rat food, neither of which contain trans fat. Even before we knew the health effects of trans fat, including it in one group but not another would be an obvious confounding factor. I would say any older animal or in vitro studies haven't lost any validity.
Studies on humans have to be epidemiological for ethical reasons, so it's harder to control for trans fat (and a whole lot of other things), especially since many processed foods are high in both saturated and trans fat. Evidence from epidemiological studies is usually combined with animal and in vitro to support for conclusions about causation, so these findings are a little sketchy to start out with. This study re-evaluated a bunch of older epidemiological studies to better control for various confounding factors. It found no link between reducing saturated fat intake and reduced risk for heart disease and stroke in humans. So maybe saturated fats aren't damaging our bodies as actively as we once thought.
From a practical standpoint though, even though saturated fats may not hurt your health, they are not thought to actively help it, whereas polyunsaturated fats are thought to decrease risk of heart disease and stroke (based on in vitro, animal, and epidemiological studies). If you increase your intake of polyunsaturated fats without decreasing your intake of saturated fats, you'll increase your total caloric intake, which would increase your risk of obesity and other associated health risks. So, even if saturated fat is benign, I would still argue that it makes sense to cut back on it to make more room in your diet for polyunsaturates.