Hi,
The https://github.com/contao/contao-manager uses Composer to update the installation.
The manager just work fine until it gets to the post-install-cmd Script of the composer.
Contao is using the PhpExecutableFinder to get the php binaries. If the open_basedir is set is_file(PHP_BINARY) is false.

Here the contao issue contao/manager-bundle#57 for more information.