I have a single source and my main config is based on overided sourcetypes.
So is it save to build all configs (FIELDALIAS, LOOKUP, REPORTS) under this overrided sourcetypes?
FIELDALIAS, LOOKUP, and REPORT are all search time configurations which are perfectly acceptable to run on a sourcetype which is set via TRANSFORMS or sourcetype= property on a particular source.
But note that of course non-search-time configs (TRANSFORM, TZ, etc, see http://www.splunk.com/wiki/Where_do_I_configure_my_Splunk_settings%3F for a non-exhaustive list) won't work with those, and note that if you use the "rename" directive to override a sourcetype, no settings (including search search-time) can be applied.