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My UBD colleague, Adrian Clynes, explained it to me: Ali is a general-purpose Malay name, while Baba refers to someone Chinese (as in Baba Malays, who are in fact ethnically Chinese). So Ali Baba refers to a company that seems to be headed by a Malay but is actually run by Chinese; and it has nothing to do with the tale of Ali Baba and the Forty Thieves.
Then I asked my year-four students if they knew what it means. Most had no clue, though a few thought it might be about something that is not quite what it seems, and only one knew that it refers to a company whose ownership is hidden; but even she could not explain why the term Ali Baba is used.
It is interesting that the newspaper uses a colourful term like this which local people are not familiar with; but then my fourth-year students are taking an English-medium degree, and almost certainly none of them ever read Media Permata. So I guess this article is not really intended for them.