I just dive-bombed an answer on meta.physics.SE (I moderate Physics.SE, so the flag is binding) with an offensive flag. When this is done on the main site, the user loses 100 rep. (see http://meta.stackexchange.com/a/22175/178438)
Shouldn't meta-offensive-flagging have a penalty attached as well? The same goes for spam flags. Suspensions are linked on main/meta, so it makes sense that all other penalties are transferred over as well.
As far as I can tell, the rep penalty is currently falling into the "hidden" meta rep (used to check for Mortarboard/Epic/Legendary badges and probably calculates the "participation" score in
Hmm, this seems to actually be a bug. Quoting http://meta.physics.stackexchange.com/faq#reputation:
(Please note that offensive penalties, if levied by the community through spam or offensive votes on your posts here, will affect your reputation on the main website.)