What are the implications of enabling 'Element' access for creating content?

You can use Elements to create content but we don't recommend doing so for multiple reasons.

We don't recommend using Elements to create content for many reasons, including:

• There will be no separation between the content and the layout. You can think of using Elements for content like writing HTML into CKEditor. It's flexible but not very scalable.
• If you've used elements to create design and layout across many pages and need to make a design update, you will need to make the update page by page. If you had used components, you'd only have to update the component and it would propagate to all pages
• Elements provide access to much more functionality than you would typically provide a content editor. For example, the Styles tab. Using this they can really start to affect the appearance (for good or bad) of everything. 
• If you are using a translation provider (or plan to in the future), content in elements will not be sent to them. Only content stored within components is exported to translation services.
• If Site Studio introduce features in the future, like access to Layout canvas content via the JSON API, this will only access content within components.

What's the alternative for flexible layout creation?

If your site requires a very flexible content layout experience you should consider creating components that are separated into Layout components and Content components. Layout components provide the layout and structure of your page. Content components then provide the individual items of content to place within the layout components. For example, you could create 1, 2, 3, and 4 column layouts components to house Text, Image, Video, Button and other content components.

To create Layout components you will need to use Drop zones within the components for content to be placed within. For more information, see Adding drop zones to a component.