RJ, thanks for taking a look at this; I'm still working on the rough edges of how to present my string of snippets and suppositions/conjectures.
I don't think it's necessary to assume that Thomas had two wives at the same time (although it is conceivable). Here's how I imagine his timeline:
1660 -- Thomas is baptized at Port Royal.
c. 1680 -- Thomas marries an unknown first wife, possibly in Maryland or maybe in Bermuda. Thomas is involved in the family's shipping enterprises, trading with Maryland and Virginia and probably Caribbean islands. The Durham family has a long-standing relationship with boatmaker William Smoot (Sr.) of Charles County, Maryland, who builds and repairs pinnaces (landing and utility boats) for Bermuda mariners -- every ship needs a pinnace.
1681-83 Thomas and his first wife have sons Richard and Samuel. (The name Richard comes from Thomas's maternal grandfather; presumably the name Samuel comes from Thomas's wife's family.)
c. 1684 -- Thomas's first wife dies, and within a year Thomas marries Dorothy a niece of William Smoot (Jr.) of Richmond County, Virginia. It is possible that her apparent (but not proven) father James Gilbert was also from the Bermuda Gilbert family, as he doesn't seem to fit into the Maryland Gilberts. Further research is needed.
1686 -- Thomas's daughter Mary is baptized in Richmond County, Virginia. Thomas's father is still alive (and still having children) at this time; presumably Thomas continues as a mariner. Thomas plans to leave his eventual Bermuda inheritance to eldest son Richard (as required by law), and knows that he needs to find a way to provide for second son Samuel as well as any younger sons by his second wife.
1690s and later -- Thomas continues as a mariner, getting eldest son Richard established in his own right, making regular business trips to Bermuda where his widowed mother (and her second husband?) are living in the house that will come to Thomas after her death, and that Thomas's son Richard will eventually inherit. At the same time, Thomas arranges with his mother-in-law and her brother William Smoot (Jr.) to provide land that will eventually go to youngest sons Thomas and John. Son Samuel, as a teenager, presumably goes to live with Smoot step-relatives in Charles County, Maryland; he witnesses the wills of two Smoot descendants in Charles County in 1704, just as he comes of age. Then he marries the step-daughter of a well-to-do man who in 1705 gives Samuel a farm in Stafford County, Virginia.
Samuel is now independently set-up in a different county, so there is no need or reason for Thomas to mention Samuel in his 1711 will (probated 1715), which has the major concern of ensuring that youngest son John receives the land that the family intended for him, skirting the law of primogeniture. Any mention of Samuel in the will would just bring up another primogeniture headache, and Samuel was already taken care of outside of Richmond County (as was eldest son Richard), so there was no mention whatsoever of them in Thomas's will.