National Institutes of Health (NIH) Medline Plus website has the same recommendations as the FDA, broken down by age, sex, and pregnancy status. They cite the 2010 Institute of Medicine (IOM) report Dietary Reference Intakes for Calcium and Vitamin D which is very comprehensive and can be downloaded for free.
The report says that:
mean calcium absorption (also referred to as “fractional calcium absorption,” which is the percentage of a given dose of calcium that is absorbed) in men and non-pregnant women—across a wide age range— has been demonstrated to be approximately 25 percent of calcium intake
However, calcium absorption or bioavailability depends on many factors such as: age, sex, pregnancy, metabolic status (such as obesity), Vitamin D intake (promotes absorption), phytic acid and oxalic acid intake (inhibits absorption), amount of calcium intake itself, etc. See p. 38 of the IOM report
In addition, some things increase elimination of calcium from the body and can also reduce absorption, such as: alcohol, caffeine, and high protein consumption. See the NIH Office of Dietary Supplements page for calcium for more.
Lastly but importantly, this 2010 article in American Journal of Clinical Nutrition directly discusses your question concerning how biovailability is taken into account when establishing Dietary Reference Intakes. For calcium, it says the dietary factors considered were phytate and
oxalate intake (both of which inhibit absorption).