I think that for some unknown reason, Thomas changed his name slightly when he appeared in Iowa, which is why you are having so much difficulty.While you know him as Thomas C. Miller, I believe he was originally Thomas E. Milton.
He left just enough clues -father: Jacob E.; mother Mary Stout; birth place either "Davis" (Daviess Co.) Indiana, or Vincennes (Knox Co.) Indiana.Birth month-February.
Jacob E. Milton married Mary C. Stout in May 1884 Daviess Co. IN.
1900 Steen Twp. Knox, IN (Steen Twp borders Daviess Co.) Melton/Milton, Jacob 36 Jul'63 IN IN IN-married 16 yrs Mary 35 Jun'64 IN TN IN mother of 2, 1 living Thomas E. 16 Feb'84 IN IN IN (Unclear whether Jacob was really Thomas' father, as it appears that Thomas was born before their marriage.)
Thomas married Stella V. Ketchem 2/26/1903 in Daviess Co. IN.
1910 Knox, IN Milton, Thomas 26 IN IN IN Stella 26 IN Catherine 5 IN Bernard 2 IN
According to Stella's remarriage record (1914) to William Joliff, she was divorced from Thomas on Sept 13, 1912.
Here's Thomas' parents in 1910 1910 Elmore, Daviess, IN Milton, Jacob E. 46 IN IN IN Mary C. IN TN IN mother of 2, 1 living
Jacob & Mary did not die until after 1930, so it would seem that Thomas disavowed his family, or didn't know where they were on his WWI draft registration, when he said he had no known relatives.