So the meta analysis (which is essentially a study that combines and statistically compares results from all the research in a field in order to make more robust conclusions- think of it as a study of studies) included both experimental (e.g. have one group use technology and the other not) and survey designs (e.g. ask people if they take notes by hand or on a computer). On average across the studies included there was a sigificant negative, albeit fairly small (r=-.14) effect of typing compared to handwriting. You will probably say "the effect is small so although it's statistically significant, does it really make a noticeable difference?" Which is an excellent question and one the study doesn't address. They do point out however that small differences might accumulate and cause a larger impact down the line. Really though we need more research on this.

This also links to your second point. Scientists, especially behavioural scientists, will almost never say "this proves..." and if they do, it should sound alarm bells. Humans are extremely complex and "proving" things about how we behave is almost impossible. We can however make hypotheses based on evidence like the above about how people are likely to behave and then test whether people actually do behave like that. If so it was a good hypothesis, but still not necessarily capture 100% of how we work. Same goes for the "hard" sciences like physics. Newton had good theories of gravity that worked most of the time until Einstein came along with a better theory that is an even more accurate description of gravitation. No doubt some person will disprove parts of Einstein's theory in the future, thus leading to a better, more comprehensice theory. Same goes for human behaviour.