Six Hundred and Thirteen Mitzvos

It is evident from the Gemora (Nedarim 25a) that accepting an oath to fulfill the six hundred and thirteen mitzvos is exactly the same as accepting an oath to keep the entire Torah. Reb Avi Lebowitz hearos wonders if this is really true. Firstly, the Ramban at the beginning of sefer hamitzvos discusses the possibility that the six hundred and thirteen mitzvos is not an actual count and it is not necessarily accepted by all sources. Even if we are to assume that our Gemora holds of the six hundred and thirteen mitzvos idea (as the Gemora in Makkos seems to indicate) as do all the Rishonim who list the mitzvos, aren't there still other "mitzvos" in the Torah that are not counted in the six hundred and thirteen mitzvos? There are many mitzvah concepts that would qualify as "ratzon ha'torah", even if not an absolute obligation, and by only accepting the six hundred and thirteen mitzvos, we would seemingly not be accepting all the thousands of other points that the Torah wants us to accept! How can the six hundred and thirteen mitzvos be the same as an oath on the entire Torah?

Reb Yossie Schonkopf suggests that the six hundred and thirteen mitzvos is the root for all mitzvos and as such encompass all of Torah.