The general question is impossible to answer, but in the specific case of Consider Phlebas I can make some guesses why the publisher did not insist on renaming it Mask of the Changer or Quest for the Lost Mind or some similarly pulpy title.
First, Consider Phlebas was published in the UK. For whatever reason, publishers in the UK seem to have a higher tolerance for allusive or quirky titles. In this answer I looked at detective novels with different titles in the UK and the USA, and there was a consistent pattern of UK titles being changed by the US publisher in ways that clarified the genre of the book. For example, Agatha Christie’s Five Little Pigs (alluding to the nursery rhyme) was renamed Murder in Retrospect in the US, and John Dickson Carr’s The Seat of the Scornful (alluding to Psalm 1:1) was renamed Death Turns the Tables in the US.
Second, Consider Phlebas was published in the UK by Macmillan, which at that time (mid-1980s) did not have a line of mass market science fiction novels. They published some Russian science fiction in translation, but translated works are an up-market segment in English-speaking countries. So Banks’ editor at Macmillan probably did not feel under any pressure to ensure that the novel was marketable to science fiction fans.
Third, by the time Consider Phlebas was published in 1987, Iain Banks had already had considerable success with three mainstream novels, The Wasp Factory (1984), Walking on Glass (1985) and The Bridge (1986). All three have substantial genre elements (Wasp Factory horror; Walking on Glass science fiction; and The Bridge fantasy) but they were marketed as mainstream novels and attracted a substantial audience as such. Banks’ editor at Macmillan could be confident, based on the complexity of Banks’ work, that this audience would not be put off by a title alluding to a very well-known line from The Waste Land.