How should I structure my CV since my degree doesn't reflect my primary studies? As per the title, how should I structure my CV since when I'm done with my course of study my formal degree (PhD, Computational Science and Engineering) will not reflect my course of study and research (environmental modeling and sustainability). Based upon my projected coursework I will get a graduate certificate in sustainability along the way. Furthermore, most of my publications will be related as well. 

Currently my goal is to secure role in academia, ideally a professorship, but my background is industry so I'm used to automated application filtering, it is a concern of mine. As such, how should I structure my CV to reflect my actual research interests, or is this effectively a non-issue in the long run?
I have a PhD in Computer Science and work in social sciences so have a similar situation as you. I get away with it as a 'methods' person rather than a 'subject matter' person. In the long run, it will be a non-issue because your research interests and jobs that interest you should overlap. But for the first post-doc position, you may need to be careful in your presentation.

First, an academic CV looks nothing like an industry CV. Get hold of some CVs from more senior academics and peers and attend any training offered by your institution. There is usually considerably more detail in an academic CV (sometimes excessive, which gives the impression of insufficient analytical skills to assess relevance).

While I am not specifically familiar with the US context, based on UK and Australia it would be unusual to use any sort of application filtering past the basic level of 'do you have a PhD'. It is important though to include your thesis title, which hopefully reflects your interests.

Any application process will include your publications. Almost all will have some sort of 'research statement' or cover letter etc. Take advantage of these to emphasise the relevance of your research and experience to the particular job. While it is fine to have a standard CV, you need to actively think about why you would be good for the particular job, not rely on fairly empty stock phrases. It is very important to write this statement or letter from a blank page for each job.

Interdisciplinarity is also attractive, but only if it's relevant - being able to use different methods is a plus in a larger research group because there's not much point in having multiple researchers with the identical skills and knowledge.