In manual mode you still have all verification methods. Have a look at the specification at draft-ietf-acme-acme-01 for more details.
The LE server has to access your server like any normal visitor. And he has to use the normal domain (example.com) for this. The reason is that this is one easy way to verify that you are really the owner of the domain - that's the aim of every validation challenge. That's why you cannot push the LE server a different IP/domain to connect to, because the thing it wants to verify is not that you own a (random) server,/domain but that you own exactly the server/domain for which you want to get a certificate.
As I already said another method is to use DNS validation where this challenge does not happen at the server level, but before that.
This method and the webroot domain verification method are AFAIK the only ones, which you can currently use without restarting the server.
Apart from that you can just run the LE client on the real server (and IMHO it would also be the easiest way) instead of doing this on some other server.
Maybe it would be a good idea for you to tell us why you actually want to use the Raspi and not the real server and we can look for more specific solutions than commenting on general things like this. Especially as this discussion at the end is not really much related to the topic implied by the headline and mentioned in the first post.
I dont mean a random sever but I have a serverr that is acting a the webserver for the domain and that is not in the same network etc as the raspi. like my raspi is at home and the server is at some hoster. I get the challenge from the raspi copy ot to the server LW checks the domain (lands at the server) sees the challenge and finish. why shouldnt that work?
It always depends on how you describe it. This is much more detailed, so I can say: Yes it should work.
Of course you can manually create the challenge on your Raspi and copy it to the real server. At the time when it’s on the real server it’s all okay, as the LE server can access the domain.
I just know no reason why such a complicated step would be necessary as you can just run the LE client on the real server, but yes it’s possible…
But before I'm talking rubbish - as I'm not really sure whether the webroot method would work in this case - I've created a new topic to discuss this independently from a Raspberry Pi:
Edit: Webroot method is not suitable for shared-hosting.
okay I just got my beta and ran LE which worked rather easy even with manual mode, I thought it was a lot harder, I just got that insecure SSL stuff which was fixed by 3 lines in the le-auto, wo no big problem, next I try to check on CSR usage, but that’s another topic.