Can you post the estimate, please?
Yes, a replacement rocker will be welded on. Preferably STRSW, but plug welded will work also.
Insurance adjusters miss stuff ALL THE TIME !!!! It is their job to miss stuff truthfully.
If you found a good shop they will create a supplement and do the job correctly.
Visit the body shop. Bring a box donuts and a case of water. Trust me on this.
Express your concerns and show them the cracked seam sealer. As long as you didn't that it to the insurance preferred shop the shop should be on your side.