"Does this bird fly?"
The correct grammar for "Is this bird flying?" is actually 「この鳥は飛んでいますか？」. The verb 飛ぶ can never conjugate into 飛んって. The rule for all う-verbs ending in む, ぶ, or ぬ is that they conjugate to て-form by dropping the final かな character and adding んで. Thus, 飛ぶ becomes 飛んで. The only time that a verb's て-form is ～って is if it is an う-verb ending in つ, う, or る, and even then, you wouldn't add an ん to it. An example of this would be 待つ becoming 待って.
I'm not sure that I understand your underlying question, so apologies if I'm misinterpreting you, but the sentence "Does this bird fly?" is distinct from both "Is this bird flying?" and "Can this bird fly?". "Is this bird flying?" is asking whether the bird is flying right now, whereas "Does this bird fly?" is more along the lines of whether the bird flies at any point in time. And, "Can this bird fly?" is asking whether the bird has the ability to fly, which would yield a different answer to "Does this bird fly?" if the bird had the ability to fly but chose not to do so (granted, a bird wouldn't ever choose that, but you hopefully see my point).