third: it is not surprising that pdf(la)tex and lua(la)tex would find different fonts. i've never understood lualatex font lookup, and can't help there. furthermore, the actions taken by the two engines after a font is found are different.
it appears that latex and dvilualatex take different actions on virtual fonts. latex compiler does not read vf files (virtual fonts management is left to dvi driver), while dvilualatex compiler reads vf files and expands them. kpsepath debug log from latex run: kdebug:fopen(/usr/local/texlive/2015/texmf-dist/fonts/tfm/public/mathdesign/mdbch/mdbchr8t.tfm, rb) => 0x299cbb0 kpsepath debug log dvilualatex run: kdebug:fopen(/usr/local/texlive/2015/texmf-dist/fonts/tfm/public/mathdesign/mdbch/mdbchr8t.tfm, rb) => 0x436ab60 kdebug:fclose(0x436ab60) => 0 kdebug:fopen(/usr/local/texlive/2015/texmf-dist/fonts/vf/public/mathdesign/mdbch/mdbchr8t.vf, rb) => 0x4379e10 kdebug:fclose(0x4379e10) => 0 kdebug:fopen(/usr/local/texlive/2015/texmf-dist/fonts/tfm/public/mathdesign/mdbch/md-chr8y.tfm, rb) => 0x437a370 kdebug:fclose(0x437a370) => 0 kdebug:fopen(/usr/local/texlive/2015/texmf-dist/fonts/tfm/public/mathdesign/mdbch/md-chr8t.tfm, rb) => 0x436be80 kpsepath debug log from dvips run on file produced by latex: kdebug:fopen(/usr/local/texlive/2015/texmf-dist/fonts/vf/public/mathdesign/mdbch/mdbchr8t.vf, rb) => 0x210ea00 kdebug:fopen(/usr/local/texlive/2015/texmf-dist/fonts/tfm/public/mathdesign/mdbch/md-chr8y.tfm, rb) => 0x211fb70 mdbchr8t.vf maps to md-chr8y.tfm and md-chr8t.tfm: (MAPFONT D 0 (FONTNAME md-chr8y) (FONTCHECKSUM O 11370565725) (FONTAT R 1.0) (FONTDSIZE R 10.0) ) (MAPFONT D 1 (FONTNAME md-chr8t) (FONTCHECKSUM O 12501363516) (FONTAT R 1.0) (FONTDSIZE R 9.962616) )