We don't actually know how much of the Yana backstory was true. He ran off to the end of the universe, but his claims of being found as a child could have been invented. He could have just been there a few decades, handful of heartbeats to a timelord. Unlikely the Doctor met him though.
I know, still if he did spend only a few decades among the refugees than he would have still been aging at a normal human rate, as he was turned human by the chameleon arch. So even if it were a younger version of the Jacobi incarnation, it's likely Jacobi himself would be too old to play him.
Although, I have read a few compelling theories to suggest Yana really was a separate incarnation from the Master who fought the Time War. Of note, John Simm's ring has thirteen stars on it (representing a Time Lord's full life cycle) with three bolder than the rest, perhaps indicating the Simm incarnation is the third of this particular regeneration cycle. Meaning that after the Eric Roberts incarnation we have an unknown War Master, Yana, Mr. Saxon, and now Missy.
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