There would only be a problem if they disabled some functions in the compilation, and if they did that, they would know that they would have unhappy customers and get less money, so NO it will not...
As for that Unix and Windows based function theory, there are NO Unix only functions, if there is, direct me to a link and I'll be able to tell you a way that would work on both Unix and Windows. (You should never have this problem though, because in the 3 years I have used PHP I have not discovered ONE...)