Ok so finally after some blood, sweat and tears I finally fixed our SAML integration issue on mendix hybrid applications. My issue was 2 fold:

1. We use a custom guest user login page in which apparently the config.ui.customLoginFn function asigned in entry.js is never called. To solve this I included the following script in our login page through a JavascriptSnippet. Kudos to Remco Snijders for his scripts here 

var  mxMobile = {};

mxMobile.enableSamlLogin = function() {
    var register = function(){
        if (window.dojoConfig.ui.customLoginFn && typeof(window.dojoConfig.ui.customLoginFn) == 'function') {
            console.log('enableSamlLogin: config.ui.customLoginFn available');
            window.dojoConfig.ui.customLoginFn();

        } else {
            console.log('enableSamlLogin: config.ui.customLoginFn NOT available');            
        }
    }
    mxMobile.waitForDojoConfig(register);
}

mxMobile.waitFor = function(fnCondition, succesCallback, errorCallBack, timeoutMs, interval) {
    var waitTime = 0;
    var id = setInterval(function() {
        waitTime += interval;
        if (waitTime > timeoutMs) {
            clearInterval(id);
            errorCallBack();
            return;
        }
        if (fnCondition()) {
            clearInterval(id);
            succesCallback();
            return;
        }
    }, interval);
}

mxMobile.waitForDojoConfig = function(fnCallback) {
    mxMobile.waitFor(function() {
        return window.dojoConfig;
    }, function() {
        console.log("enableSamlLogin: dojoConfig available");
        fnCallback();
    }, function() {
        console.log("enableSamlLogin: dojoConfig not created");
    }, 60000, 10);
}

mxMobile.enableSamlLogin();

2. The second issue I ran into was a ClassNotFound exception in the current cordova in app browser 3.0.0. and cordova-android 1.7.3 which is included in the current mendix hybrid-app-base which was fixed after I upgraded to 1.7.4. I will also log a ticket on github for them to look at this. If this is not resolved by the time you experience a similar issue do the following to upgrade cordova-android to 1.7.4:
   1. do a “npm run platform:android” as usual.
   2. this will create package.json file in your .\build path.
   3. Edit the above file and change "cordova-android": "7.1.3" to "cordova-android": "7.1.4"
   4. remove/delete the android folder from .\build\platforms path.
   5. “npm run platform:android” again.

Hope this helps someone in the future!

Schalk,  I implemented this code in our application to get SAML working on mobile for a custom login page as well.  It did resolve the issue with the mobile app and SAML logins are now working.

One question though – in my browser console I am seeing the following error:

HTMLSnippet_widget_HTMLSnippet_0.postCreate
mxui.js?636928216015980052:67 HTMLSnippet_widget_HTMLSnippet_0._setupEvents
mxui.js?636928216015980052:67 HTMLSnippet_widget_HTMLSnippet_0.executeCode
mxui.js?636928216015980052:67 HTMLSnippet_widget_HTMLSnippet_1.postCreate
mxui.js?636928216015980052:67 HTMLSnippet_widget_HTMLSnippet_1._setupEvents
mxui.js?636928216015980052:67 HTMLSnippet_widget_HTMLSnippet_1.executeCode
mxui.js?636928216015980052:67 HTMLSnippet_widget_HTMLSnippet_1.evalJS
mxui.js?636928216015980052:67 JDEAccountSync.AnonymousLogIn.dataView5: fetching object through microflow 'JDEAccountSync.DS_LogIn'
mxui.js?636928216015980052:67 enableSamlLogin: dojoConfig available
mxui.js?636928216015980052:67 TypeError: Cannot read property 'customLoginFn' of undefined
    at register (HTMLSnippet_widget_HTMLSnippet_1.js:5)
    at eval (HTMLSnippet_widget_HTMLSnippet_1.js:38)
    at eval (HTMLSnippet_widget_HTMLSnippet_1.js:27)
HTMLSnippet_widget_HTMLSnippet_1.js:5 Uncaught TypeError: Cannot read property 'customLoginFn' of undefined
    at register (HTMLSnippet_widget_HTMLSnippet_1.js:5)
    at eval (HTMLSnippet_widget_HTMLSnippet_1.js:38)
    at eval (HTMLSnippet_widget_HTMLSnippet_1.js:27)
mxui.js?636928216015980052:67 JDEAccountSync.AnonymousLogIn.dataView5: received 1 objects 
[e]
mxui.js?636928216015980052:67 HTMLSnippet_widget_HTMLSnippet_0.update
mxui.js?636928216015980052:67 HTMLSnippet_widget_HTMLSnippet_0._executeCallback from update
mxui.js?636928216015980052:67 HTMLSnippet_widget_HTMLSnippet_1.update
mxui.js?636928216015980052:67 HTMLSnippet_widget_HTMLSnippet_1._executeCallback from update

From my interpretation, the window.dojoconfig object is created and the enableSAMLLogin function is called, but when it tries to evaluate the

if (window.dojoConfig.ui.customLoginFn && typeof(window.dojoConfig.ui.customLoginFn) == 'function')

test, it fails.  Are you also seeing this on your custom login page?