That was likely the initial idea, with previous hints pointing towards it airing during a December-March hiatus of OUAT and Adam and Eddy mentioning that the show would be akin to American Horror Story, with each season having a beginning, middle and end, but who knows how much of it is still valid?
The show now has a timeslot in ABC’s regular schedule and it’s getting quite a bit of attention, being second only to Agents of SHIELD in expectations, it might turn out to be a series as regular as OUAT after all. I wouldn’t worry about the 13 episode order, that could very well be because OUATinWL is a new show in a timeslot not very gentle to ABC these last few years; for all we know, we might get the last 9 as ratings prove to be satisfactory.