In nearly every case, when you are mastering a track, leave any editing of the head/tail of the track until after you have applied any dynamics processing and EQ. Likewise, don’t fade your track in or out before you apply dynamics/EQ processing.
Applying limiting/compression can change the “shape” of a fade in/fade out, and may also change where you want to trim the head/tail of the track. In most cases you’ll want to leave those operations for near the end of the process.