Generally you after-start-up is not a very good place to run your CI tests. You cannot debug the after-start-up and you have to run your tests every time, even when you are just doing a quick restart.
Depending on how much time you want to invest you might consider a script that uploads your build to your test environment automatically and then calls the CI microflow as a web service. The Mendix Cloud Portal has an API for uploading mda's that you could use for this. That would require a lot of customization on your end though.