Today we don't treat the second day of yomtov as a "maybe it's yomtov"; it has been rabbinically enacted for us (non-Israel-dwellers) as a full-fledged yomtov.
The Talmud established long, long ago that rabbinic law has the power to order someone to be passive rather than fulfill a Torah obligation, e.g. not putting on tefilin on 2nd day yomtov (or not blowing Shofar if Rosh HaShanah is on shabbos).
I see your question is "the custom is done the way it was done then." Actually no; back then, a visitor to Israel would keep one day. While Rabbi Emden insists that should be the case today as well, Rabbi Feinstein says that when the practice was fixed its parameters changed; now you follow your hometown instead. Similarly, Ritva says that today, the borders of Israel with regards to 2nd day yomtov are the Biblical ones, even though back then it all had to do with where they could send messengers (much closer to the Talmudic borders).