I've put probably 100 hours on the WhipMOD and Reference LOD already and haven't noticed a dramatic change in the sound signature yet.
You wouldn't, unless you burn-in without listening, because the improvements are gradual, but quite noticeable. I always do offline burn-in, with 50-hour checkpoint sessions to evaluate progress.
This first experience with Rockbox makes me wonder why Fang hasn't allowed coders to develop a version for the HM-801?
Only he can answer that, but some of the limitations of the controller chip he uses in the current design cannot be overcome by modding the firmware/OS, such as the lack of gapless playback. I do, in fact, prefer the iTunes database management master/slave synch model with a large music database. If you think about it, it's the only way to keep both the master library (on your computer) and the replica (on our iPod) the same with a minimum effort. If you want FLAC playback capability within iTunes and use a Mac, you can get a copy of the Amarra Jr. for $79 which is good for up to Redbook resolution and bitrate.
The HM-801 is still going to have its uses, but I'm seeing myself mostly using the WhipMOD for day-to-day listening. The Whip (with my Protector) is smaller than the HM-801, holds 200+GB more music, and has a more powerful interface. While the HM-801 may have a more spacious soundstage, with more air in between instruments and (based on my preliminary impressions) more fine detail, the WhipMOD presents a more immediately accessible and involving sound signature.