The disadvantage to your opponant is that by mixing non-PT boats in with the PT boats your AC will now attack both. PT only TFs can only be straffed by fighters. If they are mixed with any other ships they will be attacked like a regular ship.
Is this true? I have seen 'PT boat' squadrons of CL, DD, even BC, and my AC refuse to attack at all. A great tactic for 'evacuating' ships from PI in the first few turns. The only time the AC attack is after the squadron has been engaged by a surface fleet and the non pt boat units are damaged and break of into regular surface combat TFs to withdraw.
Very frustrationg when force Z turns my invasion fleet into scrap metal, and my AC do nothing but smile and wave because the TF is officially 'PT boats'.