If you could kindly point the broken links our outdated we would greatly appreciate. We have done a refreshing process of our Knowledge Base tutorials, but of course it is possible we have forgotten something.
All the links here, supposedly work: https://theme.co/apex/forum/c/themeco/kb/
Now back to your questions.
On X > Theme Options as you found in the Header and Specific Stack tabs you will find the options to customize your header, if you don't find the option, like for example, to customize the header items background on hover, you can do via CSS, you can add the CSS to X > Theme Options > CSS
That said, I would like make you aware of our second product, PRO Theme, which offers incredible Header and Footer builder which allow you to build extremely customizable headers like no other theme on the market.
If you decide to go for it, you can access your Apex license page and pay the difference to upgrade.
Regarding your customization question, X can be customized like any other theme which follows the best WP standards.
Hope it helps