Why don't conduit fill rules apply to cables encased in closed-cell foam?
The foam isn't the issue, but a lack of spacing can be

Foaming NM cables into a wall (or otherwise burying them in thermal insulation) isn't considered to be an issue, provided that the cables were originally run in a manner that maintains proper spacing between them.  However, not all installers are that careful, and for those who aren't, they find themselves staring at the third paragraph of NEC 334.80:


  Where more than two NM cables containing two or more
  current-carrying conductors are installed in contact with thermal insulation without maintaining spacing between cables, the
  allowable ampacity of each conductor shall be adjusted in
  accordance with Table 310.15(B)(3)(a).


This covers the issues with mutual heating that you allude to when the current-carrying conductors are actually adjacent to each other, such as when a bunch of NM cables are run together.  However, with the cables spaced out properly, they will sit separated by thermal insulation, which prevents the cables from heating each other up.