1.
Sanitation. With water carry, bottles have no advantage. Reservoirs stay just as sanitary. They do not require cleaning every day, nor do they need to be dried.
As with plumbing, it is the change of water and water flow through frequent use which keeps bottles, reservoirs, and tubing fresh and sanitary. With normal use, both bladders and bottles are constantly refilled and emptied That keeps them sanitary
UNLESS contaminated water is introduced, or other fluids with sugars (juices, energy drinks, soda pop, etc.) are put into a bottle or a reservoir.
While working for the local public health district, I did a review of the literature, which I again did in 2016. Comparisons of bacterial contamination levels between bottles and hydration bladders were indistinguishable -- both had equally low rates of bacterial contamination. And both were at about equal risk for developing significant levels of bacteria and mold if not cleaned and dried properly prior to storage. In the last few years, the hydration reservoirs have become more modular in nature and have wider openings to access the water compartments, making it much easier to clean and prepare for storage than previous generations of the product.
One example study, from 2009:
https://www.wemjournal.org/article/S1080-6032(09)70419-3/fulltext
When it is time to store bottles or bladders away for the season, they can be sanitized if desired with a bit of bleach added to the final rinse water during cleaning. It is not necessary, but there is no harm in doing so. Then they can be rinsed out and be allowed to dry.
Molds and other nasty things occur if either container is stored
with water over a period of time, or have contained other fluids which might have sugars and then are not properly washed out prior to long term storage. Mold may also form in the shorter term when fluids with sugars are exposed to warmth and sun.
Also, not all discolorations are harmful molds. Most times, it may be an algae growth from leaving stagnant water exposed to light