Opening a pdf file from the command line
You have a couple of problems here.

First, the message ""can’t be opened because it is from an unidentified developer" refers to the application.

Open Skim from the Finder and it will pop up a dialog telling you it is from an unidentified developer. Click on OK. Now open the "Security &amp; Privacy" pane of System Preferences and under the General tab you will have the option to open the application anyway. Click "Open" and the app will open. You only have to do this once.

Second. Open a PDF in Skim and zoom it to the amount you require to be able to view it with your vision problems. Turn on or off the Contents and Notes panes as desired. Now select "Use Current View Settings as Default" under the PDF menu.

Now when you open a PDF in Skim it will be at the right zoom settings so open -a Skim.app example.pdf will work for you.