Just for the record, the issue with our application has been resolved by adding
Mo/builder.pm and Mo/default.pm to %INC:

https://git.luns.net.uk/configutils.git/blobdiff/ee32e725c51d18cf8189322b1bb9ff9dbe4d4c55..9c509205b570e6392331bfffa38d6cfdb5d7e347:/configbuild/bin/configbuild.in

This fixed all test errors I had before (apart of a one very minor error 
related to output sentences order). So, as I expected, YAML lib caused all the 
issues.

Also, my collague pointed me at a similar bug in CPAN tracker:

https://rt.cpan.org/Public/Bug/Display.html?id=75390

It does not seem correct that libyaml-perl somehow depends on Mo.

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