What would actually make sense would be to do a build for every version with ONE js- and ONE css-file that are minified.
I'm all for doing this instead as it makes much more sense but honestly I think the best thing to do is absolutely nothing. Don't bundle all the files together at all. Yes you'll have a lot of HTTP request to reach out for the first time a user logs into the manager, and then every subsequent visit within the manager those many requests are cached. Remember, the /manager is a interface not a website. The same best practices do not apply.
It is more configurable if they are separate but it is also more future-forward. HTTP/2 basically does away with the notion that HTTP requests are costly and we need to work around them with concatenation. Regardless of that, the server should not be concatenating and it definitely shouldn't be minifying scripts. For a front end developer, it's very frightening to know that some random server environment could malform your scripts and break everything.
For MODX 3, I'd like to work on a proposal for how the manager loads assets because I think it should support loading common assets from a CDN. This is something I've spoken with Skytoaster about. They log into many many MODX managers a day, as I'm sure many of us do. Imagine if the bulk of the manager assets were cached just by logging into another MODX site...