Simulate Overprinting - set On as default - Acrobat Pro DC

You can set Simulate Overprinting to be turned on automatically. It will have to be saved as a Custom Setting:

1.  With a PDF open, go to Print.
2.  Click on the Advanced button at the top of the Print window to open the Advanced Print Setup window. The Settings dropdown at the top of the window should show Acrobat Default.
3.  Click on the Simulate Overprinting check box and Acrobat Default changes to Custom.
4.  Click the Save As... button to the right of the Custom dropdown.
5.  Name your new setting and click the OK button. The Settings dropdown now shows your new print setting.
6.  Click on OK to close the Advanced Print Setup window.
7.  Print your PDF.

Every time you print a PDF from this point forward, your new print setting will be selected by default. It will only change if you change the Setting dropdown to something else.

I've been playing around with the for a while now. Im using a Mac, I think I have the fix.

It's the printer diolog rather than the Adobe Settings that you want to change.

Print... > Advanced > output > Simulate Overprinting.
Check that box off and you are good to go, it will save the settings as defult. 

Acrobat Reader/Standard x/Pro
On a PC:
Go to Edit > Preferences 
Select Page Display.
Under “Page Content and Information”, the “Use Overprint Preview” dropdown menu, confirm or change to be set to Always.

Open the Output Preview dialog in Adobe Acrobat Pro in order to view all available visual preview options. To get there, click on the “Tools” tab, then scroll down to “Protect & Standardize,” then finally click on “Print Production.” In the right-hand pane, click “Output Preview.”