How come you would need to separate grounds and neutrals in the main panel?
The neutral must be bonded to ground at only one
location, the first disconnect. Before the transfer panel was installed, the first disconnect would have been in the main panel.
Now that there is a whole house transfer switch ahead of the old panel, the transfer switch is now the first disconnect and is the place that neutral/ground bond must be located. Beyond this point (i.e the original main panel), all neutrals and grounds must be separated/isolated .
These are the shortcuts many generator installers take to cut down on install time (not saying this was the case here).