I don't like the term 'merge' since we never see a hint of Schala's personality, thus making me think that Schala 'gave up' her soul to create Kid. So, instead of thinking that Schala 'cloned' herself to make Kid, I think that she made herself reborn (I'd really like to see if Lucca acts particularly kindly to Schala to make her want to send herself/Kid to be found by Lucca).
So, in a sense, I do think that Kid 'merges' with Schala at the end, but in a different sense; I think that Kid accepts that she is Schala, and then either gives up her body (Kid) to return to Schala (I haven't decided if, once this happens, Schala will have Kid's memories), or retains her body (Kid) but reunites with Schala mentally (once again, either keeping both Kid's and Schala's memories, or maybe just Schala's)...