100mg is probably the amount of Magnesium (Mg) in the total molecule (MgO). Then after that you take into account bio-availability. Magnesium Oxide's bio-availability is around 4%.
Yes, 100mg is the elemental amount of magnesium in the pill, which excludes whatever counterion it's bound to. The 4% bioavailability of MgO
is a myth. The correct number is more like 20%. I'd check the documentation for Cron-O-Meter to see how supplements are supposed to be treated. RDAs are based on the amount of substance that you are supposed to consume, not the amount that is absorbed, so it implicitly factors bioavailability in already, although the bioavailability of food source minerals and supplemental minerals may be different, perhaps by a lot.