Shiurim - safek derabbanan l'kula?

The gemara (Nidah 58b) quotes R' Abahu that all safek shiurim are l'hachmir except for a safek shiur k'gris by kesamim. Rashi explains that shiurim are halacha l'moshe m'sinai, so this halacha is really nothing more than a restatement of the rule that safeik d'oraysa l'chumra. It also implies (Rashba spells this out) that the rule would not be true only by a gris, but by any derabbanan.
The gemara in Brachos (30) has a safek whether the shiurim for davening times are ad v'ad bchlal or ad v'lo ad bichlal. Tos. asks what the gemara's safek is - we should adopt the stricter shiur because safek shiurim l'chumra. From Tos. question we see that Tosfos disagrees with Rashi - tefila is a din derabbanan, yet Tos. still felt we should interpret shiurim l'chumra. Tos. would ostensibly learn that this is a special kula by gris.
According to Rashi, it is a bit difficult that we require a restatement of the basic rule of safek d'oraysa l'chumra and safek derabbanan l'kula, but even more difficult is Tos. - why should we go l'chumra by all sfeikos of shiurim even by dinim derabbanan?