However there's at least one bug as described above. If you have to remove directories and quit the application completely to be able to import and "synchronise", even if only sometimes, that's a bug. Also I have some difficulty understanding why, assuming you've allocated a root directory to LR, you then have to keep reminding it to "synchronise" in order to include whatever you've just put in it.
You really need to try to understand what LR does and how it works. It won't just 'find' files* you've moved around on the disk, you have to import them into the catalogue.
Using the word 'synchronise' is not helping here. LR uses this term for finding 'lost' files (ie that have been already imported) that have been moved by utilities outside LR or had their metadata changed outside of LR (eg by editing in ACR in PS).
Using terms incorrectly will only confuse you further and prevent others from helping you effectively.
If you use LR to move the files from the camera/card to your computer in the first place, everything else will fall into place. You have complete control of where files go, LR can build all it's previews and you can get some basic keywording done in one process.
Once the files have been imported, then you can manage them using LR.
As for dupes, of course they aren't a good idea in principle, however I sometimes deliberately create duplicate files for reasons that make absolute sense to me, and not just in backups.
It might make absolute sense to you
, but if no one else thinks that makes sense, including Adobe's engineers, you're creating problems for yourself. There's not a lot you can do to a RAW file other use it as source data, if you did edit it's contents it would be prudent to change the file name anyway. Don't have duplicates around and things will become less confusing.
The fact that LR4 doesn't display the entire RAW file is a real nuisance too...... - I'd forgotten what aspect ratio I'd set, nominally...
This isn't really a LR issue, but more concerned with the curiosity of why you'd want to use anything less than the full frame size. It makes a degree of sense if you're shooting OOC JPGs, but once you've decided to take advantage of RAW format why apply a crop in camera ? Just leave the camera's setting to use all the sensor, then crop in your RAW converter.
Old fart time.
Trying to use out dated and ineffective practices in a new workflow paradigm just makes it more difficult for you. Take the time to learn how LR works, then drop inefficient work methods and let LR help you work more efficiently. I'm sure all of us 'old hands' using LR have had to adapt their work to suit LR, but it makes working digital photographs more efficient, fast and, as a result, you'll find it easier, more productive and enjoyable.
*There is a function to have a 'watched' folder, but that's more intended for use when doing tethered shooting in a studio, so probably best to avoid that option for now.