The visa type makes a difference in determining whether they are a residents or not, for example, students with F-1 visa do not count their days in the first 5 calendar years, but once the individual passes the substantial presence test and is a resident, then her tax filing is the same as a US citizen.

In this particular case, the person with R-1 visa is not an exempt individual, and the child born in the US and has an SSN, so as long as the taxpayer passes the substantial presence test (most likely he does) and therefore is a resident, I do not see any difference between him and an American with a nonresident alien spouse.