Oof... lies to children. I'm not sure why I'm getting involved if you cannot listen through the lines... Anyway, it is a theological physics nomenclature issue.
Most of the video is sound and useful to, e.g. a high-school student; and a diplomatic critic might even call the pion jazz at the end of the video, min 5:00 et seq, sensible, provided the pion rhetoric is understood, by HEP physicists, to vaguely mean chiral symmetry breaking in QCD (χSB). But not, not pion condensation as she garbles in min 6:00!
She mumbles she has a background in nuclear physics, and, indeed, nuclear physics has been veering into "hadronics", a hybrid compromise between QCD and nuclear physics methods. I am not familiar with specific papers she might be alluding to, but there is lots of preaching on such things in YouTube videos...
In it, she said that the real story is pions... Is she right? Is there a detailed list of the various contributions to masses,... no matter how technical?
There is no "real story", beyond a technical understanding of χSB in QCD, a subtle story. Lattice gauge simulators of QCD provide technical lists of contributions, e.g., cf. this; and both HEP and nuclear physicists concoct models emphasizing the salient features of the picture... arm waving with math, with which physicists feel more comfortable.
In my favorite picture (cloudy bag models), in a small region near the confinement radius (the boundary of protons and neutrons), the sea quarks have condensed effecting dynamically broken chiral symmetry: thereby coupling to almost massless "pions" (pseudogoldstone bosons) and enhancing the masses of these quarks by a factor of 50-100 thus turning them into some type of "constituent quarks", three of which comprise the p and the n. Dodgy and flakey, ill met by moonlight.
Whether you can morph this quark condensate to a "pion condensate" in contiguous language is something you might not be that keenly intrigued by. Or shouldn't be. Conflating quark chiral condensation with pion condensation would roll eyes in most circles I work in.
P.S.: Does the mathematical term 'trace anomaly' mean they aren't sure about the amount of contributions from each source of mass??
No, this is a hyper-narrow technical term of the QCD coupling running with its strictly quantum (this is what is meant by "anomaly") β-function associating to the trace of the energy-momentum tensor dynamically breaking scale invariance. (Trace is the summation of repeated indices in that tensor...) "We" are pretty sure, provided we fully appreciate the meaning of the technical terms involved.