If you are running LC on windows platform, you can get the same output as generated by Acrobat using GeneratePDF service by using the Acrobat conversion route.
Use the following steps to enable Acrobat route.
1) In LC AdminUI go to following location
Home > Services > Applications and Services > Service Management
2) Select GeneratePDFService from the list of services.
3) Set the following property to true :
Use Acrobat Image Conversion (Windows Only):
Try an image conversion. You will get exactly the same results as produced by Acrobat.
On non-windows platform I am afraid there is no option to change this. The difference is due to the difference in MediaBox created by PDFG and Acrobat. The actual image dimensions embedded in PDf are the same for both.