You can safely apply it to the whole track, and only move transients as needed without having other sections of audio affected in any way. But keep in mind that when you move a transient you're stretching/compressing the audio between that transient marker and the previous one which will affect the sound - though not the timing - of the previous hit to some extent. And you want to make sure there aren't any hits without markers in that region or they'll get moved with the stretched audio.
If you want to be sure, you can phase-invert a clone of the track, and check that the cancellation of hits that aren't moved remains total. Just make sure no FX are active, as the phase inversion can affect the processing.