Cid suggests that while Shinryu was not intentionally based on Midgarsormr, that when it was summoned Midgar's influence on dragon legends in Eorzea may have indirectly caused similarities.

As for the toy, I was expecting some kind of sign that Omega's 'soul' somehow found its way into it but I don't think that actually happened. calls it a 'toy that follows you around' so I think it following Alpha is just what it was made to do. Though Omega giving up the combat thing and following Alph would have made an interesting ending.