I'll also go from JB 6.1 to JB 7.0.4 on my iPad soon. I started with a JB on my iPhone which is already 7.0.4, just to make sure everything's there and works before I transition the iPad.
So if I want to start with a clean iPad, I simply (after DFU) choose not to restore from backup?
Ahd if I do restore from backup, will it also restore Cydia tweaks and settings from 6 (which would become visible only after jailbreaking it in 7), or does it only restore "official" content (so even after DFU+restore, the iPad will only have official file-system contents plus apps, no leftovers whatsoever)?
Yes, putting iOS 7 on the iPad (with DFU method) will make a clean install; you'll have a fresh-from-the-factory iPad if you choose to "Restore as New."
In fact, restoring from new guarantees there will be nothing left from old jail breaks (vs restoring from backup). Sometimes, bits and pieces of coding from jail broke tweaks do get left behind, tho they are not usually an issue on a stock iPad. But, if you don't put a backup on, it won't get the bits of coding. So, putting iOS 7 on the iPad will make it stock. There will not be any jail break coding on it.
As for tweaks, they may have made a backup for themselves. What I mean is, if you install a tweak you had on iOS 6, you may find some of your tweak settings are still the same, even though you are on iOS 7. It's the same as if you put an app on the iPad from the AppStore; it'll sometimes "remember" how it was. But, you have to be jail broken and re-install that tweak; it won't happen on its own. Hope that makes sense...
On a related note... How come installing iFile wants to remove some icon pack for Zeppelin (that was on the jailbroken 7.0.4 iPhone)? I've encountered a few of these strange phenomena (installing A wants to remove seemingly unrelated packages X, Y etc.). Not sure if it's a transient issue due to incompatibilities...
Not sure on this one, so I'm leaving it alone. Hopefully, someone else can help.
And one last thing: Does Cydia cross-check packages versions between all available repos, or just within the repos from which the respective packages were installed? So if you install package 1 from repo X, it will only check its updates from within that repo (and not from repo Y, or others if they become available)?
(I noticed some are available in more than one repo, and if I add one that includes betas (rpetri.ch for example), then it adds to the confusion a bit.
No, versions of packages are not cross checked in different repositories. Each tweak will only go back to its repo to see if there are any updates.
For the multiple lists, just ensure you install the one that has the best chance of getting updated. For example, if you want to run a beta update, you'll run the one from that repo (Petrich's, for example). If it gets updated, only that tweak will get updated, not the one on the main repo. And, you'll get that red badge to tell you it has an update. But, the non-beta tweak (usually on one of the default Cydia repos) will not get the update.
Hope this helps.
Marilyn