While selecting the parent for the custom module here https://github.com/phpbb/phpbb/blob/3.1.x/phpBB/phpbb/db/migration/tool/module.php#L215-L218 the query doesn't take in account that thre're more than 1 modules with the same module_langname.
For example, there're 3 ACP_MANAGE_FORUMS modules. The query takes the [random] 1st row from the result to set as parent, which may lead to wrong extension ACP/MCP/UCP module placing.
Module categories have no module_basename and module_mode which can be used to correctly select them.