From your description, yes, it seems to be overkill, for whatever reason the developer chose to do this.
It sounds like an extremely large job to undo and rework what was done, in fact, it may not be possible at all.
Field groups should be separated by functionality and not what template they are on, for example a “Hero” field group that is applied to templates where it is used and allows you to make changes in a single field group.
I’ve been sitting here trying to think of how to guide you, but the issues is too complex. There are a few things that you can do. What I would do would depend on the budget I have to work with.
More than likely, assuming the client does not want to rebuild the site from scratch, I would work with what is there for existing pages and build in a more logical manor for anything new that needs to be added, if and when it needs to be added. This will mean a lot of duplicate work making sure that you make changes to everywhere where changes need to be made. As I was making changes I would look at what could be combined, for example the use of template parts for common things and other places that I could reduce duplication on a case by case basis.
