Sharepoint - CSRListForm and PreSaveAction or PreSaveItem

The problem you were having is because you weren't using the standard save button. The standard save button looks kind of like this:

<input name="somereallylongname" value="Save"
    onclick="if (!PreSaveItem()) return false;if (SPClientForms.ClientFormManager.SubmitClientForm('WPQ2')) return false;//etc" 
    id="somereallylongname"
    target="_self" type="button">

Notice that the onclick event starts with if(!PreSaveItem()) return false;, and then it does if (SPClientForms.ClientFormManager.SubmitClientForm('WPQ2')) return false;. You said you're doing:

SPClientForms.ClientFormManager.SubmitClientForm('WPQ2');

to save the form, but that's only a portion of the logic, removing much of the validation. If you had done:

if (!PreSaveItem())
    return false;
if (SPClientForms.ClientFormManager.SubmitClientForm('WPQ2'))
    return false;

from your own button, validation would have worked the way you expected, including PreSaveItem. All OOB forms in 2016 are CSR forms, and they still work fine with PreSaveItem/PreSaveAction.