How do I trust a self-signed certificate in iOS 10.3?
I've identified that the specific parameter that Apple looks for when allowing you to manually trust a certificate is the CA Basic Constraint (E.G. critical,CA:true). If the certificate has this extension, the system will allow you to manually trust the certificate.
However the process has one extra step (as opposed to iOS 9.3):

Export the certificate as PEM format
Send the certificate to the device (Safari, Email, AirDrop, etc...) and open it
A message will appear telling you the profile has been downloaded. 
Open the settings app and tap the &quot;Profile Downloaded&quot; item below your Apple ID row. 
Install the Certificate. You will have to provide your devices passcode. 
Navigate to Settings -&gt; General -&gt; About -&gt; Certificate Trust Settings
Enable full trust for your certificate