In the $1,100 & up range for Intel laptops from major players, Thunderbolt is not all that rare.
In the sub $900 range it is. Up until very recent that sub $800 zone is where the overwhelming vast majority of AMD laptops were. That is going to change a bit with The new Ryzen 4000 options, but the "low priority" was more so because it was 'cheap as possible' priority more so than whether Thunderbolt (TB) was useful or not. TB isn't aligned with race bottom system pricing.
Atom never was most of the Ultra-Mobile space at all. The Celeron/Pentium chips aren't Atom based. A very large fraction of the Chromebooks aren't on Atom anymore either.
Even though AMD was (is?) larglely regulated to the lower half laptop segment they didn't have much leverage in the Chromebook space. How much work the chip vendor puts into reference design and system R&D support matters. Intel largely swapped out their Atom for Core based designs in the lower-mid range Chromebook space and kept ARM implementations from sweeping them away. There aren't zero ARM solutions there, but ARM didn't sweep Intel away like a plague of locusts either.