Yes. Certainly sand those areas down and fill again. I'd avoid making the mix too wet as being water based, it could shrink a bit. Don't try and do too much at once. Several thin layers rather than one thick layer.
Before changing the primer colour, why not try spraying some scrap wood with the primer and the daphne blue topcoat? If it comes out the colour you want it, then leave it as is. Most Fender colours were simply sprayed over initial heavily thinned clearcoats, sometimes over undercoats (there was very little consistency over the years), some over stained bodies, but in the pre CBS-days (and probably for a while after), finishes often got sprayed on top of other finishes - even sunbursts, sometimes to quickly turn around a custom colour order, sometimes because the original finish was flawed. The prime colour is the topcoat, underlying colours (unless very dark) will have a very small effect on the final colour. There is no one defining 'daphne blue', as the paints often came from different manufacturers and even DuPont's shade varied slightly depending if it was nitro or acrylic paint. Some finishes have faded a bit, so they are more like a sonic blue, whilst others have not (depending on both the paint type and the clearcoat used) and are significantly darker than what would be called daphne blue today.
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