JonDonym has the same configuration for http and SOCKS settings: 127.0.0.1:4001

Supposing one were to change the system proxy settings to 127.0.0.1:4001 for http and socks.

Some apps prefer to connect with http, not socks.

How does the app distinguish between the http and socks settings? They both use the same IP and Port.

How can 127.0.0.1:4001 be both http and socks?

So does this mean that an http app would connect to 127.0.0.1:4001 the same as a socks aware app?

The app is parsing the proxy settings (it usually starts with the more specific proxy types if there are any) and it stops on the first proxy type it is supporting (that may be HTTP for one application and SOCKS for an other). Then it starts either speaking HTTP with JonDo or SOCKS. Thus, the destination (127.0.0.1:4001) does not matter here at all. (Of course, there might be bugs in the apps in this regard (like: https://bugzilla.mozilla.org/show_bug.cgi?id=527478) but that is not related to your question at hand)
Because JonDonym (and with it JonDo) is supporting both.
No. They connect to the same destination but are not speaking the same protocols.