The .vmdk file and the location within this file to which data is written depends on the location to which the guest OS writes its data. Therefore VMware Workstation opens all files in R/W mode which causes at lease the time stamp to be updated.
What might be an option to minimize the data to be uploaded to your backup target is to create a snapshot. Once created you need to backup all files, and then keep backing up only the modified files. Once the snapshot grows to a certain size, you may consider to consolidate/delete the snapshot, create a new one, and start with a new full backup.
André
