Yeah, 100Mb isn't terrifically fast, so a short discontinuity doesn't count for much. You don't have to worry much about characteristic impedance if the PHY, transformer and connector are nearby.
A ferrite bead is much very different than a few inches untwisted, though. For that to work, it would at least have to be a high frequency, low impedance type, not an average wideband 100 ohm (or whatever) type; in which case it wouldn't do much for EMC anyway.
I wouldn't suggest playing with EMC on the PHY side, because it's supposed to be individual 50 ohm traces, not differential, at that point. (Except where the termination resistors join, which is 25 ohms Thevenin equivalent. Those should be right by the PHY to minimize stub lengths.)
The magnetics handle EMC by using balanced matching transformers and common mode chokes. Additional ones could be added if there's imbalance at high frequencies (i.e., poor common mode rejection). You can get connectors with this built in, saving board area. They're actually fairly ugly inside (untwisted lengths, anyone?), but as long as it meets spec...
Tim