Do countries get the list of every passenger that's transiting their airspace?

To answer the part of your question I quote here:

I wonder if the Belarus intelligence was handed the manifest as a routine or they somehow got access through it using spyware?

This particular operation was done with HUMINT: Roman Protassevitch was physically followed into the airport and up to the counter by an agent who queued up directly behind, and snuck photographs of documents being presented.

At that point, the agent turned heel and walked away from the line. Protassevitch noticed all this, and notified friends of the encounter, presumably before boarding the flight.

Protassevitch continued on the flight anyway, perhaps not knowing an EU internal flight would cross Belarus.

Aside from the fighter jet, there were also three intelligence service agents who rode the plane also. One could ask on aviation.se whether such agents would have the means to force the aircraft to divert to an enroute airport.

from Hacker News https://ift.tt/3vjxP2C