I would advise against using clear CA to hide the gaps in the binding and rosette in this case. CA works wonderfully with darker woods, especially rosewood. On lighter woods like your cypress and spruce, CA darkens the wood considerably. Yes, you could seal with shellac and then apply the CA; you would end up with a level surface, but the transparent CA won't hide the gap. I would try mixing different color wood putties until you find a close match, and fill the gaps with this. Once sanded and level, you could even draw a few grain lines very carefully with a thin marker if needed. This helps break the outline of the fix. As always, you should try it out first on a piece of scrap. If done carefully, it could be almost impossible to spot under the finish.
I have also seen some opaque dyes you can use to color the CA. I have never tried these out, but it might be another option (if you can find the right color). Perhaps some other forum members have tried this and can give you further advice.
Please let us know how everything turns out.