The missing works are good but shouldn't make your decision one way or the other. You can get all his unpublished works on this CD which is very good and cheap:

https://www.amazon.com/Inedits-Messiaen/dp/B00000JLND

So if you are leaning toward the performers on Warner's box I would go with that.

The big difference makers for me are:

• The 5 CDs of Messiaen playing his organ music and Loriod's Catalogue d'Oiseaux are essential and hard to find elsewhere
• The "landmark interpretations" CDs on the Warner box contain some really good performances

A note on the 5 organ works CDs on the Warner box: 4 of them were recorded in the 1950's in mono. More recent versions in better sound exist, which may or may not be important to you. But if you want to hear OM himself, this is the way to hear it.