Not sre I understand all of your problem but I will try:
1) If you have FCP 7 you can now apply a transition to all your clips in one operation. Just select an In and an Out to define the range and add the default transition of your choice. (selecting all clps also works)
2) If what you are trying to do is systematically remove frames at top and bottom of each edited clip because each clip is made of all the captured material, then I am afraid there is no other solution that to trim each transition (this is after all an editing software).
sorry if I completely missread you…
patrice