physiologically, the rationale behind breathing with the dantien (and I assume that the one in question is the lower dantien - there are three - you can "breathe" into all of them, so to speak; in fact, going a bit further, one can even "breathe" down to /with the soles of the feet
) is in order to maximize diaphragmatic excursion during inhalation, since, if one is an upper chest breather, one is using accessory muscles of respiration excessively (scalenes, sternocleidomastoid, upper traps, pecs), and one will actually inhibit the degree to which respiratory diaphragm can contract; this is not uncommon for many people who live in a chronic "stress response" phase; so, for qigong purposes at least, the concept helps shift awareness to where you want RD to go, so to speak;
now, if is one doing "natural" (Buddhist) breathing, then the awareness typically stays in the dantien throughout the entire length of the breath; if one is doing "reverse" (Taoist) breathing, then the awareness travels a bit differently (if one has opened the Microcosmic Orbit, for example, it can follow that pathway);
RD first contracts on a relatively stable ribcage, causing the central part, the dome, to descend; this movement is limited by both upward pull of mediastinal elements (stuff in the thorax that attaches to it) and resistance of the abdominal contents below (which will vary depending on if one does "natural" or "reverse" breathing); once the RD has stopped descending, then the central part is stable, so when the fibers contract they are now elevating the mid to lower ribs, expanding the thoracic cavity (the rib movement is triaxial, resulting in a hard to describe but easy to demonstrate motion); also, the external intercostals, braced on a stable thoracic spine, will elevate the ribs; levator costarum and paraspinals are also involved then all the accessories as well (46 muscles in total!);
this is a good general descrption of respiratory biomechanics;
this is about ribs specifically
the best pictures are in Kapandji, Physiology of the Joints, Vol. 3
never heard this bit about the RD atrophy; I would suggest that the degree of neuronal activation would decrease as opposed to actual atrophy of muscle fibers;
I'm surprised a PT was even talking about it, TBH! They barely mentioned anything about this stuff in school, and most PT's are so obsessed with the lumbar vertebrae that they don't even consider how the RD impacts things like low back pain (which is funny, considering how treating RD will often clear up dysfunction of the head, neck, low back, etc.)