This seems obvious to me, and I'm not sure why it wasn't mentioned before. 
Yes I created my account to post this. 
Why not just modify her idle stances a bit more and just make her Samson, OR, somewhere in between. 
Samson is designed to be a giant juggernaut character, what if, during the cloning process the DNA from Filia and Samson became one new creature. Rather then being of two separate minds, with one dominating the other off and on, what if the new clone is somewhere in between? 
You could add some of Samson's current art and stances, it would fit the world properly without being an obvious clone character and it would explain the modified playstyle. 
my 2c.