I know what you mean and its a concern
In the past I have found it works well as long as you dont try and use it to fill a massive gap and if you do - to do it over a few goes.
I left it proud when it dried which I hope will allow some room for shrinkage.
If it all goes pear shaped then I will add a post to the forum about 'Relic-ing my kit guitar' and say it was my plan all along.