Unfortunately the Preflight app doesn't allow inspection through Safari. I'm following the instructions found here: Hyperlinks in AEM Mobile which is actually unchanged from the DPS Classic method. So, it appears to me that Adobe has some bugs to work out. These links worked just fine in DPS Classic (Adobe Content Viewer), so I really don't think it's my code.
I'm afraid I can't share the folio due to client confidentiality policy, but here is the code that sets up and triggers the links (I pass in a value like "first," "last," or a number):
setLink : function(setWhere) {
var jumpLink = document.createElement('a'),
linkHref = 'navto://relative/' + setWhere;
jumpLink.setAttribute('href',linkHref);
jumpLink.setAttribute('id','jumpLink');
document.body.appendChild(jumpLink);
setTimeout(function(){
document.getElementById('jumpLink').click();
},125);
},