There appeared to be a consensus in the threads I could find prior to the release of the Battlemech Manual that Ultra and Rotary Autocannon would get the TN bonus from a Targeting Computer even when firing multiple shots. However the language appears to have been clarified in the Manual to prohibit this.
Specifically Targeting Computers say they do not provide a benefit to any weapon making a Cluster or Flak attack (pp114), and the definition of Rapid-Fire weapons specify that when firing multiple shots in a single attack, the attack is considered a Cluster weapon (pp97) as opposed to earlier language where rapid fire weapons were described as resolving like a cluster weapon.
This would seem to indicate that you only get the TN bonus for Rapid Fire weapons if you only fire a single shot. Am I correct in this interpretation?