You are using physical in a rather broad sense.
"Also, if apt-get update
ing my Debian system has any effect at all on a computer's functioning, presumably it must change the physical structure of the computer (that's the only way processing can change). So why would this news about a bug in X.org which makes the monitor explode be news?"
Very little is currently known about the cerebral characteristics that underlie the complex processes of meditation as only a limited number of studies have addressed this topic. Research exploring structural connectivity in meditation practitioners is particularly rare.
We knew already that meditation changed the concentration of neurotransmitters and blood flow in the brain, but not that it changed the white matter. At least, that's what I gather from the abstract; I don't care enough to pay for the full article.
It's new science. Hence news.
EDIT: This is the same distinction gwern made in their analogy below, but perhaps more explicit.
http://www.sciencedirect.com/science/article/pii/S1053811911006008