Does Mixcraft have a "punch-in / punch-out" feature?

As of version 6, yes.

Instructions for older versions:

• Cut out the unwanted section of sound.
• Arm another track and click Record.
• When recording reaches the appropriate spot, play the replacement riff.
  
• Stop recording.
  
• Trim the new recording (if necessary) and then use the up arrow to move it into place on the original track.

Remember in Mixcraft, you can always have an extra track to work with. Not all the sounds have to stay on the same track.