Is the dictum of safek dioraisa l'chumrah (and its inverse safek d'rabanan l'kulah) a principle from the Torah, or a din d'rabanan? How does this change how we react in these sefeikah situations?
The Rashba (Toras HaBayis, Bayis 4, Shaar 1, 11b. Also in his chiddushim on kiddushin 73a d"h mamzer vaday) says it's a Torah principle. The Ran (Kiddushin 15b according to the Rif pages) also holds it's a Torah principle.
The Rambam (Perek 12 in hilchos tumas hames, halacha 12) holds it's a principle from the Rabbis.
The Pri Chadash (Klalei sfek sfeka, klal 1) and the Kreisi U'Plisi (beis hasafek, d"h ke'she'ani) paskin like the Rambam. The Shach (klalei sfek sfeka 25), Pri Megadim (on that Shach) and Toras HaShelamim (klalei sfek sfeka hamechudashim 16) paskin like the Rashba.
This is only a partial answer to your question, but hopefully these sources will be a start.