The Reference manual states there is a Punch Type recording in Pattern mode (page 105), but it doesn't come up on my screen? Only Step, Replace & Overdub.
Also, when Step recording in Pattern mode, the Arp doesn't work, only in Replace or Overdub recording?
(I love the Arps on the moX, but they are very difficult to use with the sequencer.)
Punch Record only becomes available for realtime Record in Song mode. Never in Pattern mode. In Pattern mode Replace, Overdub, and Step are available. If you need to punch in you can move your Pattern data to a blank Song, punch in your data, the move the data back to your Pattern.
Moving data back and forth between modes allows you to take advantage of feature found only in a particular mode. Song mode is linear in nature and therefor allows things like Punch-in/out.
This is explained in detail in the following article: One SEQUENCER Two Modes, Many Related Jobs
If you get stuck, post your questions here.