Last night, I perused the Gough/Hoover cemetery book, and the only thing that I found was that the Allen, Texas, Cemetery backs up to Cottonwood Creek. I then checked out Pitts' "Collin County (Texas) Cemetery Inscriptions" Volume 1 and the only Thomas's listed are:

Thomas, J. W. b. 1860, d. 1937
Thomas, Nannie E. b. 1869, d. 1943

No Bunches are listed as buried in Allen. After that, I checked my database and found that I had Mary Elizabeth Thomas (dau. of John Kinchloe) and husband Louis Henry Wells buried in Cottonwood Cemetery, DALLAS County, Texas. I then went back to the USGS site and searched the whole state of Texas for a Cottonwood Cemetery, and low and behold one came up for Dallas County, southeast of Wylie and east of Sachse, just south of the Collin County line. I think this is the one you're looking for. Check the link below which will take you to the location of the cemetery. From your description, I think this is it.

Unfortuately, I do not have the tombstone inscription book for Dallas County cemeteries, but this should give you somewhere to go.