The checks for these two programs passed in 2.1 and I believe in early 2.9 versions but not at the moment.
Each check finds the binary in the expected place, but the Simple Test fails.

I regularly upgrade my TeX Live distribution, so it's possible that the behaviour changed there but I just didn't notice at the time. I'm currently using the 2017 distribution.

If I manually execute the same commands from the Simple Test, the BibTeX command seems to fail due to the filename extension:

jeremy@EliteChook2 ~/projects/kile/src/test $ latex test_bib.tex 
This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017) (preloaded format=latex) 
restricted \write18 enabled. 
entering extended mode 
(./test_bib.tex 
LaTeX2e <2017/01/01> patch level 3 
Babel <3.10> and hyphenation patterns for 10 language(s) loaded. 
(/usr/share/texmf-dist/tex/latex/base/article.cls 
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class 
(/usr/share/texmf-dist/tex/latex/base/size10.clo)) 
No file test_bib.aux. 

LaTeX Warning: Citation `test' on page 1 undefined on input line 3. 

No file test_bib.bbl. 
[1] (./test_bib.aux) 

LaTeX Warning: There were undefined references. 

) 
Output written on test_bib.dvi (1 page, 268 bytes). 
Transcript written on test_bib.log. 
jeremy@EliteChook2 ~/projects/kile/src/test $ bibtex test_bib.tex 
I couldn't open file name `test_bib.tex.aux'


If I run "bibtex test_bib", it works.
Is that weird? Does that seems like the behaviour of bibtex changed? Because it looks like the configtest code hasn't changed materially in a long time.

I don't know why MakeIndex is failing, it returns 0 when I run it manually.