I'm a developer and I like studying other apps and how they are structured, something people call software architecture, especially for software product lines, theme of my masters thesis. This suggestion is based on the knowledge I gained through multiple projects throughout my life and also the Affinity suite itself. I'm also aware the following is true only of the Windows versions for reasons will be made clear ahead but I doubt the approach is different on the macOS version.
Here it goes.
While licensed as separate applications, the core of the Affinity application is contained in a few files (a few DLLs) shared between the multiple apps. Nevertheless, this actually means that when licensing the different application we are actulally licensing the usage of a few parts of an existing API for a particular purpose, depending on the app itself. Thus, Affinity Publisher - with both Designer and Photo functionalities incorporated - is the whole application and the easiest part of what I call Affinity Studio in this idea.
Before anyone can ditch my ideas as unfeasible because of the macOS version, I must remind that .NET Core is already cross-platform (although with some limitations) and can run on macOS and even Linux and if I'm not wrong .NET 5 (droping both Core and Framework from its name) will be released by the end of the year and may have complete support for fully cross-platform desktop applications, dropping also the need to support a separate version for macOS and opening the door to a Linux release with little to no extra cost for Serif.
Also, I don't remember exactly where but I've already heard from someone from Serif that the file format for all applications, despite the different file extensions, is exactly the same (go ahead, change the extension of a file and open it, I'll wait) so files are really not an issue but I'd suggest reducing to a single extension for simplicity (I'd go for .afp ). And we don't need to have access to the details of the file format If the exposed API provides the means to incorporate file importers/exporters (read files and create objects on the canvas and vice-versa) that could solve the biggest issue I see in the forums, support for multiple additional file formats, which anyone should recognise it may be an impossible task to accomplish by Serif alone no matter how big their team is.
If your concert is security/privacy of users, I'd state I don't really remember any platform using plugins being overly concerned about it, which I understand could be a big issue depending on Serif's values but I believe this is something the community could regulate on their own: some more concerned would work on evaluating extensions and providing feedback to us all about which are safe to use and which are not and word will eventually spread. If Serif is really concerned about security, they could incorporate the means to remotely block (blacklist) harmful plugins (please, don't tell me you dont know Apple and Google can do that on your phones).
Sorry for the long post but I see a big potential in applications like the Affinity suite given the proper means for expansion and I would love to work these ideas out without having to be part of their team itself.
I think the ball is in your court now, Serif