“The reference was first made by the Chairman about 1:05 in the tape and Justice Thomas made a reference a few moments later in one of his responses.”
Right, and the first reference made by Serrano was a joke that he was waiting for the SC to decide that a Puerto Rican was eligible to be president. This clearly was a reference to his own circumstances, since Serrano is the most senior Puerto Rican in Congress [http://serrano.house.gov/Biography.aspx]. Likewise, Thomas jokingly points out that “we’re giving YOU another option” in response to Serrano’s teasing that the Court hadn’t addressed the Puerto Rican question, but that Thomas apparently was willing to indicate it would be fine for a Puerto Rican to serve on the Court. Thomas’s allusion to “we’re ducking that question” (clearly said jokingly) was a reference back to Serrano’s original question about eligibility of Puerto Ricans to be president.
The issue of Puerto Rican statehood is a perennial one in Congress. Puerto Ricans are “statutory” citizens, but may not be NBCs.
http://www.puertorico-herald.org/issues/2003/vol7n38/Poll0738-en.html Many Puerto Ricans would like to have the full rights of U.S. citizenship, including the presumption that their children are NBCs etc.
In short, this is much ado about nothing. I don’t think anyone can reasonably infer from this exchange that Thomas is a birther.
A "presumption" of natural born citizenship cannot be acquired. It's either present at birth, or it isn't. Should Puerto Rico become a state, the children born of citizens (plural) at the time of statehood will be without doubt natural born. Refer to the so-called "grandfather clause" for precedent.