I can see where there must be great confusion on this John D. Allen.........there are so many with the same name and born about the same time frame. You did not give details that would set your John D. Allen apart from the others...such as wife's name/children's names.
Here is what I did find:
Headstones Provided for Deceased Union Civil War Veterans, 1879-1903 Name: John D Allen Col., 15 regt MO Calv buried: Spanish Fort Cemetery, Vernon, Lawrence Co, MO State of Cemetery: Missouri Date of Death: 14 Aug 1898
The same John D. Allen (same military info + 7th RE Milita) filed for his Civil War Pension in Missouri and his widow Charlotte B. Allen filed in MO for her Widow's pension. So now you have this ones wife's name.
Found this little bio on the Calvary Unit he served in: 15th Regiment, Missouri Cavalry Organized November 1, 1863, from 7th Regiment Enrolled Militia. Attached to District of Southwest Missouri, Dept. Missouri, to April, 1865. District of North Missouri, Dept. Missouri, to July, 1865.
Special Schedules of the Eleventh Census (1890) Enumerating Union Veterans and Widows of Union Veterans of the Civil War; John Allen (same military info) is living in Spring River, Lawrence Co, MO
1900 MO, Lawrence Co, Spring River Allen, Charlotte Allen 60 bn Mar 1840, MO, Widowed, 0 kids
I found 8 TREEs with the same dob/dod the only difference was some listed a wife and some did not: John Daugherty Allen Birth:23 Jul 1818 - Tennessee, USA Death:14 Aug 1898 - Lawrence, Missouri, USA Marriage:03 Sep 1842 (3 Sep 1842) - Barry, MO (Missouri) Spouse:Sarah Ann Sally JONES 2nd Spouse:Charlotte B. "Lottie" Hatfield
I viewed the original document on line for both of his marriages marriage:
Missouri Marriage Records, 1805-2002 Name: John D Allen Marriage Date: 3 Sep 1842 Marriage Location: Barry, Missouri Marriage County: Barry Spouse Name: Sarah Jones
Missouri Marriage Records, 1805-2002 Name: Mr John D Allen Marriage Date: 11 Jan 1880 Marriage County: Lawrence Spouse Name: Miss Charlotte B Hatfield
But because I dont know his children's names......there was no way to 'track'him on the census records and prove that the two marriages are the same John D. Allen or not.
I could not find a death certificate on the Missouri site for a John Allen that died 1923 in Versailles, Morgan Co, Missouri.Are you sure about the county....the year???
Hope something here will help in your search, Marsha