We don’t know if there is a mystical reason behind choosing Lyanna, such as her Stark blood, old magic, etc. What we do know is that Lyanna was unhappy in her betrothal and that Rhaegar must have had some sort of contact with her prior to and/or before he crowned her the queen of love and beauty. He chose her at Harrenhal for a reason– but again, there is nothing that details that reason, and thus we can only speculate.
The fact that Rhaegar waited until after Aegon was born says to me that he was also waiting on a verdict for the feasibility of Elia being able to have another child soon. Rhaegar appeared to have wanted to act fast, perhaps fearful that the final battle was coming soon and anxious to fulfill his prophecy.
So no, I don’t think he would have chosen Lyanna if he had been told that Elia was fit enough to carry another child basically immediately. It all happens very quickly, and with Lyanna being highborn, desperate to escape her betrothal, and having made herself memorable to him in some way, she was his best pick.