Could be because there is more profit margin on the 1.8L than the 1.5L T? That would make Atlas wish to sell more of the 1.8L variants (Oriel and Hardtop) than the Turbo.
Or simply because Atlas did a poor marketing survey, got the wrong idea, and planned their supply chain in the wrong fashion. Perhaps they did not book the 1.5L Turbo engines (and other related parts) in large enough quantities and since the suppliers will be supplying to many assemblers, it is not possible to change orders on such short notice. Poor planning could be a reason to discourage the sale of one variant and encourage that of the other. Afterall, since their clause mentions that "no refund" is possible, they are sure they won't lose any customer but can force the 1.8L upon them.
Another possible reason could be that because 1.5L Turbo requires higher grade fuel, which is not always and readily available, people will use lower grade fuel and it will cause problems. This can ruin the reputation of Civic (and consequently, Honda). It could be the same kind of thing that happened to Liana. Local ustads did not understand it and gave it a bad reputation because of mishandling it. Suzuki has never been able to recover from that and their 1.3L segment is now almost gone. Having the 1.5L for the select few who can afford better grade fuels and live in affluent areas will give the Civic and exclusivity, a status symbol, and avoid the bad reputation.