how are these messages created in the bouncer's window? Do they appear because a script contains an ECHO command which causes them to be there, or are they just normal query messages as if from a real nick?

If a script sends them there using the echo command, the echo command can use the -n switch to not have the icon be highlighted. If it's a normal query window, a remote script could created which filters the messages going to the query window, by using /echo -n to send the query message there using the -n. Something like:

Code
ON ^*:TEXT:*:?:{
  if ($nick != -psyBNC) return
  if (!$query(-psyBNC)) query -psyBNC
  echo -tmn -psyBNC $+(<,$nick,>) $1-
  halt
}


If for some reason you don't want to mess with the incoming messages, such as losing consecutive or leading spaces, you can use /window -g0 to reset the switchbar's color to normal, but otherwise do nothing with the message.

ON *:TEXT:*:?:{ if ($nick == -psyBNC) .timer 1 0 window -g0 -psyBNC }