Logically I think that sounds right, but it appears to be stopping the regex from finding anything whatsoever unless "line" is actually the first thing on the next line. In that case, it does not prevent it from continuing on to the next VTY block if transport input doesn't match in the first VTY block. If I stick with "line" or something else that is not present on the line immediately after "transport input" it doesn't appear to match anything at all.
I'm currently using a
line con 0(.*\n)*? logging synchronous(.*\n)*line vty 0
type regex to isolate the CON 0 and VTY 0 4 blocks so that I can check each individually. It just seems less elegant than, I don't know... SOMETHING else . Also it makes it so the checks for Console and each VTY have to be unique.