You'd be surprised at how cheap, relatively safe and reliable bus services are in those regions.
Source: me and my wife traveled extensively by public transport in, well, at least Pakistan. The other countries are indeed sort-of hairy, but mostly for job-clearance-related reasons.
Generally the border between Paxistan and India cannot be crossed though. I believe Attari/Wagah is the only place, and it was closed too last I heard.
To my knowledge, no. In the recent past, either you could cross via the the Wagah-Attari border crossing or get on the Thar Express train [1], which connects Karachi with Jodhpur via the Zero Point crossing. But the Thar Express has been closed since 2019.
They should avoid Pakistan if they can, not Afghanistan. It’s in relative peace while the border region of Iran/Pakistan see regular fighting between Pakistani forces and Baluch separatists[1].