###TL;DR export PATH=/usr/bin:/bin
I had a look at config.log to see where configure mentioned the paths used by the Anaconda distribution and I found 3 references to miniconda3 — 2 were related to the PNG libraries
and one to the PATH variable... of course the bin directory of the Anaconda distribution has to be prepended to PATH, hasn't it?
To be sure that was not a problem with my PATH I issued the command
$ PATH=/usr/bin:/bin ./configure 2>/dev/null | grep -qs miniconda || make
...
make[1]: Leaving directory '/home/boffi/src/emacs-26.0.90'
$
I have now a way to shade private Anaconda libraries from the scrutiny of configure, I have an instance of Emacs 26 too and eventually I have the doubt that
configure had been too smart in deducing too much from my PATH.
ps I'm not going to approve my answer because it seems to me just a workaround, I'm convinced that a better solution is possible.