I could see the song being at least partially.

In the song, the main character leaves a comfortable life and a woman he loves in Vermont for Mexico, noting "I don't know what called to me / But I know that I had to go." Notably, this mirrors elements of Winchester's life, leaving the southern United States for Canada, fleeing the Vietnam War draft, a war more nebulous in origin than wars the United States had previously been involved in, causing significant consternation about our motives and reasons for involvement.

Here's an interpretation of the song from Rock Voices: The Best Lyrics of an Era (1980):

The sensual clues of time and place are what give Jesse Winchester's "Yankee Lady" such resonance. Also from Winchester's 1970 debut album, the lyric charts the course of a season's idyll with an older woman and an initiation into manhood. Here, the simple traditional pleasures of rustic domesticity are viewed with reverence ("apple cider and homemade bread / To make a man say grace") while the joys of awakening sexuality are beatifically recalled ("And I smile like the sun to think of the lovin' / That we did"). Winchester invests this rich memory with a fully integrated poetry of passage, from wandering youth to hearth-loving and ultimately restless manhood, from season to season, from time savored to time consumed ("An autumn walk on a country road / And a million flaming trees"), while the Yankee lady of the song stands for all the comforting constancy of a land left behind.

A similar interpretation is seen in The McGill Daily Vol. 065 No. 027: October 29, 1975. While speaking of THE BRAND NEW TENNESSEE WALTZ, columnist Helena Lamed notes "Winchester combines a simple love song with a gentle lament for something left behind: possibly his country, but rather a piece of himself. 'Yankee Lady' projects a similar image."

In summary, I don't think the song is representative of something Winchester lived, but may very well be symbolic of his migratory life and things he left behind in doing it. Unfortunately, I couldn't find any direct quotes explaining his inspiration for the song, so unless someone else can unearth something, we'll be stuck making suppositions.