Tough call!
The Meta 55 is quite the different beast, in it's geometry at least - and at your height a Small Meta 55 would be the way to go.
As for the Super 4, sounds like you're right on the fence.
However, if you have short legs - you may struggle for standover on the medium.
What is your inseam?
Check it against the bikes standover on Commencals website to see how much clearance you will roughly have (fork and tyres will change this number a bit).
I stand at around 5'9" maybe 5'10" and the medium is sweet for me.
Has the store offered to fit you up on the new bike once it's built?
I would stress the importance of having the bike fitted by a professional, as you may find the Thomson straight post will not give you enough rear saddle movement.
I use a straight Thomson post on most of my bikes, since I have shorter thighs and requires a more forward saddle position. Some people are longer in the upper leg and require more layback on their seatposts.
There is a chance that straight Thomson post could be useless to you if it doesn't allow for enough saddle adjustment.
Also, if you are struggling for measurements, check out Wrench Science's bike fit calculator. Select the MTB version, get a friend to help you measure everything up and see what comes out, it can be very helpful when determining size.