Maybe I just think too complicated .
Perhaps you do
I too "develop" my NEFs with NX2, and even though I don't use a cataloguing solution yet (waiting patiently on PM to fill this in later), I still might be able give you some tips here.
First of all, I NEVER store or archive JPGs derived from NEFs; the embedded jpg preview is more than adequate for this purpose (in fact it is a 90+% quality jpg). I use this embedded jpg for all my web exporting, creating contact sheets, etc. So no problem of mixing up meta data this way.
To produce quality prints, I save the NEF as (16 bit) TIFF, and then print from Photoshop. This TIFF is also not kept/archived, again no problem of mixing up meta data this way.
Now it becomes more tricky: in case I need to perform some complex editing that can't be done in NX2, I preprocess in NX2, save the results as a 16 bit TIFF and edit this in Photoshop. This TIFF file does get filed alongside the NEF (which I also mark with a specific colour class set aside for NEFs that have a corresponding TIFF). This TIFF and NEF, I need (ok, want) to keep synchronised with respect to the metadata. So far this is a manual process, but one which I hardly ever need to perform anyway; I usually have all metadata setup before editing
and the number of TIFFs that exist this way is fairly limited (most of my editing can be done within NX2). Note: when PM's cataloguing feature is implemented, I hope it includes "stacking" images and the ability to update the metadata in all stacked images in one go (like it does now for JPG/RAW pairs).
While I do take care not to edit any RAW file metadata outside PM, my setup actually would allow for it; I have PM read xmp sidecar files first. So even when I would have edited the metadata of a NEF within, say, Camera Raw, PM will read and display the correct version of the metadata. It is also automatically synchronised between all sources whenever I update the data again in PM. (note: to help myself a bit, I wrote a little perl script to check whether or not a given TIFF is older than its corresponding NEF; these cases probably need investigating as it could mean I've edited the NEF without also editing the TIFF).
Right, so now for some practical solution for your case. First of all I would ditch the jpgs from your workflow and use the embedded preview. This would solve probably 95% of your potential problems. For the rest, if you make metadata changes in e.g. Atomic View that end up only in a sidecar file, simply setup PM to read xmp sidecars first and then "update" a dummy field in PM in order to synchronize the embedded metadata NX2 uses. You could write a little script to find those files with updated xmp but with older NEFs to help you with this step.
Hope this helps,
Hayo