This is a very good idea to add a totally new type of challenge to the game, but unneccessary big and powerful new beings as normal enemies could cause some issue in the whole Factory building and managements part of game

I would suggest turning Dragons into Arena like boss fight as a standalone minigame in Factorio
Imagine a structure in which by activating it You will have to face a boss (here a dragon) and defeat it with provided weapons and equipment. by doing so you could unlock some Technologies or it could be the prerequisite to passing certain parts of the game.

if you would like to hear more of this idea, send me a friend request on discord and we will talk more about it. ecologia