Here's what I'd do in your shoes....
Its not the technicalities, but the business aspect. So replacing something is not an easy task, no matter how lucrative the new shiny thing looks. We also have to look at resourcing / time / money. What I mean by that is, if we leave the existing WA-WAOP as is and let it do the federation tasks, then it is BAU for federation. We can purely focus on using CA Access Gateway for acting a reverse proxy for NGNIX WebServers. If we were to also include CA Access Gateway into the WA-WAOP mix, then our scope widens. This means more design, more testing etc. So my question really would be what is your immediate business needs and longer terms needs. Structure the change accordingly. For e.g. if your immediate business goal is only as Reverse Proxy for NGINX, then just use the CA AG for that. But in future you can create an additional virtual host and route federation traffic from fedsvc.company.com DNS to this new virtual host in CA AG. Again that would be a new project and effort.
As for your other question i.e. Is the only difference between our currently deployed WAOP and the SPS WAOP is New Atlanta ServletExec Java servlet V.S. the SPS Tomcat Java servlet?
That is just one of the changes. There is a lot more under the covers. As you starting working on CA AG and get familiarized you'd understand.
These are my view points and what I'd do or suggest after looking at both sides of the coin i.e. Technical and Business.