I can't use Lightroom, as the mobile version only syncs via their Cloud solution (I live in Greenland, and we actually pay pr. Gigabyte down/uploaded). So it needs to be an application where I can select individual folders and they are synced to the iPad when I sync in iTunes.
Using the iTunes application isn't the solution either. I can select folders to sync, but the folders do not expand like a tree. I have over 1K photo-folders, so keeping them in the root is not possible.
Suggestions
First, check out Photosmith. I think it's MUCH better than Lightroom Mobile for a whole bunch of reasons. For you, it does LOCAL sync so you only need your LAN. I find it much better for metadata as well.
Second, LR doesn't do iTunes sync via Photosmith. It's completely independent of that, and so I can't say what the "root" folder problem is. LR, as you know since you have it, does collections; you use a Photosmith publish serve to then "publish" them to the iPad.
Third, check out Photosmith's documentation. It has a bunch of stuff about workflows, and they vary depending on which direction you work, i.e. iPad first? or Mac? And also workflows for RAW images, which are a real pain on the iPad. I'm not sure it would work with a thousand photo folders, but I assume you don't synch all of those
Rob