Sorry, I just figured my question wasn't really interesting as nobody replied, but you're right, may be it IS interesting if nobody had the answer!
First let me simplify my case so it's easier to describe the how/to and maybe to understand:
What I wanted:
a letter H, on a RED background, playing let's say for 4 seconds
I wanted the letter to grow and finally reveal INSIDE (the letter) the footage.
But I also needed a lower third to appear behind the letter H and in front of the footage
My solution:
To take care of the footage showing in the letter:
V3: Footage --> Composite / Travel Luma
V2: Letter H, matte --> Composite / Normal
V1: Red background --> Composite / Normal
Then I the L3:
I added 2 layers to what I had created:
V5: Text (lower 3rd) --> Composite / Travel Luma
V4: Letter H Matte (again, so I have it twice on this composition)
Be careful to make sure they area no empty Video layers between your layers as it will not work (I struggled with this for a while)
Hope this helps