The fact that Qantas returned to SIN rather than stick with Dubai or move to Doha speaks volumes re where their customer base prefer to transit/connect. And those who want to transit ME still can.
I think there was more at play than just preferences for transiting SIN over DXB or DOH. Of course, not everything is about moving people between Australia and Europe. I think SIN works for QF better than ME as there is much more origin/destination demand (both business and leisure), and that provides more margin than connecting traffic. Also QF have the ability to move passengers from a SIN hub onto a carrier that they do have a significant stake in (i.e. Jetstar Asia). Not to mention I guess there would be more Singaporeans travelling to Australia for tourism than Emirati's and more citizens of each country living in the other (Australia/Singapore) than in Australia UAE).
i.e. Commercially more sensible to have a service based on both connecting and origin/departure traffic than one relying almost entirely on connecting traffic.