Thank you very much for taking your time. Yes Mike, I tried the same as you suggested and it works now. So, there is no freeze. It just takes a huge time when compared to other softwares. But, I can only get the transparency intact only when I rasterise the image before export.
What was the setting you used for your first PDF.
My work around was to open the file in Affinity Photo, then rasterise and clip the image to the size of artboard there and then come back to AD and export the PDF.
Took me like 20min. Huge difference when compared to other softwares and the file size is also 5x larger.
As you suggested Affinity should look into it. Because this is our daily work around as a print designer and time is the key.
Thank you for your help Mike and thank you for your feedback on the design :)