It may not be a very wise solution but this is what I did: in case there is <timeout> duration of inactivity, establish a duplicate connection and check in the process table whether the concerned process is still executing. If yes, do not return from read_all() because my thinking was you have not really read all.

And I am passing an extra optional max-timeout parameter to the Net::SSH::Expect::exec() which acts as a check in the loop in read_all() in case the command hangs or something.

Update: The optional max-timeout parameter serves another purpose of circumventing a flaw in the inactivity logic of read_all(). What if a command keeps on printing stuff to its STDOUT indefinitely? The default read_all() will never return in such a case.