I’d go along with your view that some of the information may have been romanticized slightly, and there are a few obvious factual errors.
The King at the time of the Battle of Killiecrankie in 1689 wasn’t just King of Scotland. He was King of Scotland, England & Ireland. And he wasn’t King James. Elizabeth of England had died in 1603 without children or a clear successor, so the English invited King James VI of Scotland to become King of both countries, known as King James I of England and VI of Scotland. So from 1603 the sovereign ruled over the “United Kingdom.” There was no king of Scotland. James I was followed by Charles II, then (after a gap) by James II who abdicated in 1688. At the time of Killiecrankie in 1689, William of Orange was King (jointly with his wife Mary, James II daughter).
One of the quotes has Frances fighting on the Jacobite side, the other on the Williamite. Obviously both can’t be correct. If he was Presbyterian then in my opinion he was unlikely to have been on the Jacobite side since they wished to restore the exiled Catholic King whose broad aim was to suppress that denomination.
Though the Jacobites won the battle of Killiecrankie, they didn’t win the war. Indeed the battle was their last success before being finally defeated at the Battle of the Boyne in 1690. So as you say, if Frances fought on the Williamite side, he was unlikely to have been banished. If he left Scotland it was probably because he chose to do so.
Throughout the 1600s huge numbers of Scots moved to live in Ireland. Initially as part of the Plantation of Ireland but in the 1690s there was a big surge due to famine, rising rents and lack of employment in Scotland. During the whole of the 1600s at least 100,000 Scots settled in Ireland, representing something like 10% of the entire Scottish population. The majority settled in Ulster. By the early 1700s, many Scots in Ulster were again dis-satisfied. There were a number of reasons. The main ones were an inability to buy their land from landlords who wouldn’t sell, rising rents, poor harvests due to repeated bad weather, weak prices for cotton and other woven products, plus some restrictions on Presbyterians ability to hold government positions. So many of them, mostly Presbyerians, moved again to North America. Today they are known in North America as Scotch-Irish, and in Ireland as Ulster-Scots. Something like 200,000 Ulster Scots moved to North America throughout the 1700s. There’s a bit of background on this site:
https://www.ancestryireland.com/wp-content/uploads/2017/08/The_1718_Migration.pdfSounds to me as though your ancestor went to Ireland in the 1690s as part of the big surge in Scots migration there at that time.
“Francis Ross was born in Thagtshire.” You’ll not be too surprised to hear there is no county of that name, or anything like it.
If Frances was genuinely a “Lord” then his pedigree should be well documented, in Burke’s Peerage or Debrett.