Ben,
Interesting. I consider the database part of Lightroom to be one of its best features. It empowers the non-destructive editing at the core of the application which really lets you do any number of edits, backwards and forwards on actual or virtual copies and always be able to get back to any step in the process while never harming a single byte of your raw file. It also lets me quickly find 'all the images I have ever taken in Rocky Mountain National Park' or 'all the images I have taken with my 70-300 L IS lens', or have an instant count of how many images I ever took with my 5DsR,' just to name a few.
As for the folders, I am not sure I understand your issue. Yes, you do have to import images before you work on them. But I always copy images off of my memory card to folders of my own naming convention and organization before I import them, at which point they are externally organized just the way I want as well as being cross referenced and accessible in Lightroom. And if I ever need to move them I just move them and then tell Lightroom where I moved them to and it is happy again.
As for LRTimelapse, it loads in your files from where you specify, but eventually you pass that info on to Lightroom so that Lightroom can import your images and edit then keyframes you have identified in LRTimelapse. LRTimelapse will eventually do some of its own naming and locating of the output time-lapse videos, which it recommends are not located in the same file as your stills you used to make the video. I have not used LRTimelapse enough yet to fully understand how it wants to organize its output files yet.
Don't know if any of that is helpful in any way. Perhaps if I still have not answered your question you can ping me again
ML