I think you have enough evidence that John & Eliza were Vern's parents, as listed in the 1900 census. Eliza would have been 50 but while births to mothers in their 50s are uncommon, menopause can happen as late as age 59.
And Missouri marriages show John and Eliza were married in Crawford County, which adjoins Dent County:
1870 Dent Co, Mo.
J D Jones 26 Tenn
E J Jones 23 Mo
W C Jones 5 "
M A Jones 3 "
1880 Dent Co, Mo. census
Johnathan Jones 36 Tenn
Eliza J. Jones 35 Mo
Willie Jones 16 "
Martha Jones 13 "
John Jones 9 "
Charley Jones 2 "