After switching to istanbul mocka.opts file was added to tests root dir.
npm test command has following inside: npm run jshint && npm run check-style && npm run func-test && npm run unit-test, where
npm run func-test is npm run build-sample-proj && mocha -u bdd -R spec --recursive test/func and
npm run unit-test is mocha -u bdd -R spec --recursive test/lib
Seems this commands are ignoring paths where mocka tests should be executed and take exec dir from mocka.opts

As possible solution separate func-test and unit-tests scripts may be deprecated. The only left is test which contain something like
npm run jshint && npm run check-style && npm run build-sample-proj && mocha