The itinerary you propose contains both a stopover and an open jaw, which are not allowed under the rules of the companion fare. Yes, you can book "illegal" companion fares online.
If you need to make a change to the itinerary, one of three things can happen:
1) you will be able to make the changes online without any problem;
2) you will have to call reservations, and the agent will make the changes without question.
3) you will have to call reservations, the agent will be rule savvy, note that your reservation is not "legal" , possibly check with a supervisor,
and may state that Alaska will allow you to keep the reservation on the original dates booked, but not make changes.

On the first change that you attempt, the probability of each of the above scenarios are probably about equal.
However, with each subsequent change, the probability will shift away from 1) in favor of 3).

If you have enough companion certs, you could simply play by the rules and apply two of them to the different segments of your itinerary.