Understood. For changing the mysql-data storage I'd have to change the datadir in /etc/mysql/my.cfg
you can do it via a custom template (see wiki for info)
Yes... I know it is most likely that I am indeed looking for trouble. But then again... from my experience the greater pain in the ass is migrating the data after a few years from one server system to the next. So I'd rather have them away from the OS 
SME is linux.. if you use its backup feature you can move to another server without problems
if you wish to move to another server o.s. you need to do what to do
using a single disk for o.s. can be done, but you need to (heavily) modify standard behaviour if you wish to keep o.s. separate from data
in any case, following the wiki page I told you and using lvm volumes you can create many mount points (/home /opt /var) and achieve what you are looking for..
it could be a good exercise but, let me say, it's not worth the resut and you will be on your own if you choose so.
I guess the usecase for a small "family-homeserver" is a bit different from a full blown company server, where availability is essential.
I guess the usecase for a small "family-homeserver" should be hassle free.. just install, configure and forgot it
moreover, storing a big amount of data on (any kind of ) a server is a bit dangerous without a backup.. this is true regardless of the use of the server itself IMHO
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