I agree with you that it would be easy to be confused by multiple Thomas Pickles. I think this all started when I was looking for cousin Thomas Newton Pickle. I have since found no less than three Thomas Newton Pickles. One of these is indicated in one of the Census records you site.
However, with respect to my original post, I am certain that the Thomas Pickle that married Lucinda B. Stephenson also married again. This is clear from the 1900 Census record which shows in the box for number of years married the number 25 and also the number 50. This would represent the 25 years he had been married to Lucinda until her death, and the 50 would represent the total number of years married, hence 25 additional years married to his second wife, who the census record calls Jennie, and who is findable in later (post-1900) Census records as Virginia. It is clear that those kids in the 1900 census could not be by Jennie, since she was 43, and the eldest sons were 37 and 34.
I have tracked the whole group by Census from 1850 (I think the pre-1850 Census records are not particularly useful for my purposes) to 1920. I think this has to be the same Thomas Newton because his youngest children by Lucinda B. Stephenson are Thomas Newton Pickle and Benjamin Franklin Pickle, born 1861 and 1866, respectively. Thomas Newton Pickle continued to live with his step-mother at least until the 1920 census, and Benjamin Franklin Pickle also lived with her after the death of Thomas, i.e., well into adulthood. So I think it very unlikely that there were two Thomas Pickles born 1820/1 who both had sons named Thomas Newton Pickle AND Benjamin Franklin Pickle who was born ABT. 1861 and 1866.
What I am not sure about is if the Will abstract I have found is the right one, although I note that one of the step-children living with Jennie seemingly lived with her throughout his life, and also that it the census records would have Thomas Pickle, Sr. having kids when he was nearly 80. I think you can see how this might have had a chilling effect on family relations which might manifest itself in the reading of the Will.
With respect to the marriages you site, there is one which fits really well: Thos. Pickle and J. C. Swiney, 10-MAY-1875, H. H. Holt, Security, married by S. N. Stephenson, pg 276. This marriage satisfies all the criteria for the 2nd marriage provided that the "J." in "J. C. Swiney" stands for Jennie, or more precisely, Virginia.