Hallo,
your post content evolved from its initial version, which is one of the advantages of this forum system. In fact, no difference is expected in regard to your case between FLUKA 4-1 and FLUKA 4-2, while the reported difference wrt FLUKA 4-0 was advertised in previous posts, starting from the original one of October 2020, and is indeed induced by the physics model improvement you point out, as indicated in the release notes as well as in the preceding forum discussion.
As a side remark, note that fluctuations below 10 keV or so are due to insufficient statistics on the low energy side of the neutron spectrum, where the yield considerably drops, as a proper lethargy plot (giving dn/dlogE - rather than dn/dE - as a function of logE) clearly shows.
You are welcome