Feeding supermassive black holes may have ended the cosmic 'dark ages' billions of years ago

[Admin]

NASA's Chandra and NuSTAR telescopes have teamed up to study a supermassive black hole-powered quasar that could have played a key role in ending the cosmic dark ages.

Feeding supermassive black holes may have ended the cosmic 'dark ages' billions of years ago : Read more

 

[Unclear Engineer]

There are a few things I would like to see some cosmology expert explain better:

The article says that photons could not travel freely across the universe until its matter had cooled enough for protons and electrons to form monatomic hydrogen atoms, because free electrons absorb photons. That is when the Cosmic Microwave Background Radiation was supposedly released as much shorter wavelength photon radiation. But, this CMBR appears to have a "black body" wavelength spectrum instead of a spectrum indicative of electrons changing orbitals in hydrogen atoms. With further cooling, monatomic hydrogen atoms are theorized to have combined into diatomic hydrogen molecules, which are theorized to have started absorbing photons, again, so that everything in the universe was shrouded by diatomic hydrogen. Then stars of black holes formed and started emitting ultraviolet radiation that once again broke apart the diatomic hydrogen into monatomic hydrogen and then stripped the electrons off the protons of the hydrogen atoms to once again form free electrons and free protons. But, in this new period of ionization, the universe is "transparent" because most of the hydrogen ions are gathered into galaxies, so their density in intergalactic space is much less than it was when the same material supposedly made the universe opaque, before the CMBR was released.

My questions are:
1. Can somebody provide a more detailed discussion of how the CMBR photons were not absorbed during the "dark ages" that followed its release?
2. Can somebody provide a better explanation of why the same amount of matter that was making the whole universe opaque while it was 1100 times smaller than it is today, is not making galaxies opaque to us now (or 13 billion years ago), when it is apparently concentrated into galaxies that have, on average similar densities ?
3. Can somebody explain to me why atoms that were in a universe where "space expanded" by a factor of 1000 or so still have the same energy levels for their electron orbital transfers before and after expansion? Does the space inside atoms not expand? For that matter, do electrons and protons not expand? If not, why not? The theories assume that the "fields" they exist in do expand, which is what the theories say gives us redshift.