The major difference between a JPG and a TIFF is that a normal JPG will only ever have 8 bit data, while a TIFF can contain 8, 16, 48 or even 96 bit data, depending on how the RGB bands are handled. So, TIFF data can allow a higher resolution measurement than a JPG, which also means a greater dynamic range of values can be represented.
Another difference is that the JPG image created by the Nikon will have been heavily filtered by the Digic. I have no idea exactly what Nikon* do, but presumably artefact suppresion with a large side order of spatial filtering feature in the dark parts of the frame. The joy of using the TIFF data is that you get to control what you permit Matlab to do to your RAW data. Certainly the JPG/RAW profiles showed signs of the background in JPGs being very harhly denoised and that might hide subtle detail
You don’t say if you have applied dark subtraction to your RAW image. If not, that would probably suppress the noise in the RAW frame a little.
As to what JPGing does: if the image compression is overdone, it can create faint square box features in some parts of the image. However, Nikon** will almost certainly apply it well enough that the squares will not be obvious in the JPG without a hefty contrast stretch, but they can – potentially – impact your photometry slightly.
For me, if I wanted to derive meaningful numbers from a dataset, I would always use the dark subtracted RAW files – but JPGs may be useful for sorting out what you want to do to the data.
Hope some of this helps. 🙂
*Or for that matter what Canon do. Both companies are reticent on the subject.
**My camera is a Canon.