Scoob, I suggest that you read the manufacturers advice as to how to seal the drains. racefanone gave you the tip that plumbers putty may stain the acylic. If that is the case with your new sink, it seems that the warning to not use plumbers putty would be included in the installation instructions. If there is nothing stated in the instructions regarding the use of Plumbers putty, I would put a small amount on the underside of the sink to see if it stains the acrylic used in the manufacture of your specific sink. If it does not stain the acrylic, then I would use it. If it does stain the Acrylic, then I would call the manufacturer and give them hell for that ommission.
If the instructions warn to not use plumbers putty, then they should tell you the proper material to be used for sealing the drain. If they do not, then call the company that made your sinks and ask them the proper method.
I share your concern that the epoxy putty may be problematic when trying to knockout the drains. The epoxy putty may be stronger than the Acrylic sink material around the drain and you may break out or crack the Acrylic if you get too physical with it. This is another good question to ask the sink manufacturer.