Your issue is nothing to do with ExpressionEngine.
The template you are uses javascript to smooth-scroll within the page. It appears to be configured properly for in-page scrolling, but not for links arriving from other pages. This is a consequence of how the scrolling utility you are using is written - it needs to check for whether it is being called at page load or not, and if so effectively force a scroll to top of page before then scrolling back to the correct location.
You can fix this a number of ways, but how very much depends on what else you are doing on the page. But you might get some ideas for a way to proceed from other discussions on stackeexchange of the issue - e.g. look at the notes to the first answer to this question - https://stackoverflow.com/questions/14804941/how-to-add-smooth-scrolling-to-bootstraps-scroll-spy-function
More generally, EE is a powerful back-end CMS that gives you total control over how the information is displayed within your website. The upside of this is flexibility, the downside is that for the most part you have to create your own templates to control what HTML is generated; but within these templates your control over how an anchor tag is created is complete. In the light of this, your final question does not make much sense. Perhaps if you clarified what you are trying to do you might get a better answer.
Anyhow HTH.