The preference in iTunes tells it where to read and write your files. It will not move the existing music library. You should set this to your HDD/Music, and you're done. Consolidate will then pick up the files you have left elsewhere (e.g. the now unblessed ~/Music) and copy them over for you.
Unfortunately, I'm almost certain there's no equivalent Dropbox solution for this currently on iOS.
While I cannot give you a technical reason why two-way syncing on iOS is not possible, I can say that at a high level, the iOS platform is more guarded in terms of allowing developers to access certain capabilities of the device.
As you stated in your question, Android devices are capable of two-way synchronization through apps like Dropsync; this is because of the relatively more open-ended nature of the Android platform for both developers and users. To read more on why this is the case, read the 'Android Offers an Open Platform' section of this article.
To confirm, I contacted two customer representatives of two data-sync companies: Loom and SugarSync. I asked both reps the following question:
Is possible for two-way synchronization of files between an iOS device and a computer? For example, if I sync pix from my iPhone to my iMac, and then edit/delete the pix on my computer, will the changes be reflected automatically on my iPhone?
Both times, the answer was:
No, this is not possible due to the closed nature of the iOS platform.
If this capability is very important for your work, I would suggest migrating back to an Android device.
If you want/need to use your iPhone for this, and if you need a platform-independent solution (i.e., you don't want to use iCloud), I'm afraid tedium is in your future. I would suggest that you keep a list of the photos as you edit/delete them on you computer, so that you know which photos have been updated and need to be manually re-download from Dropbox (or manually deleted) on your iPhone when you use it next.
Best Answer
This issue has come up in the Dropbox forum as well, with the following answer from support:
If you did a restore from TM, you should already be past the "copy the content over" step and might just see the indexing/uploading step (which shouldn't upload).