Any photos?
It will just be skinned over and I think if you do anything to it you will just make it worse.
It will need weeks to fully cure, then you can cut it back if you want but it will probably look ok under the underseal
I hope the stonechip does not attack the Jotun as it tries to dry. I had a similar problem with stonechip going on thick due to a faulty gun and lack of experience with stonechip, it acted like paint stripper on the Epoxymastic 121 underneath and had to be scraped off.
id still brush it...anyone can slap on some brush sealer and look as good as the factory the more messy and slap dash the more original it looks , not so easy to caulk on a line
okay its not what your factory did , but it wont notice to 99% of people vs a wonky caulk line will stand out to everyone
other methods ive seen are mask either side and caulk some on then smear it with a finger and pull the tape...looks neat but not factory looking