When I do yarn install --modules-folder=/usr/bin/node_modules binary links are created in ./node_modules/.bin rather than in /usr/bin/node_modules/.bin/
In previous versions, binaries were linked from /usr/bin/node_modules/.bin (i.e. subdir of modules-folder). It looks like it was broken in #3545 in particular by this commit: c5a32cc. But I'm not 100% sure.
I tried yarn 0.27.5 and 0.28.1 both have the bug. 0.24.6 works as expected.