I used evercoat OEM bead seam sealer. What you are finding in the seam is probably not bondo but the original seam sealer that has dried up and cracked. Mine looked the same. Cleaned mine out really good, hit it with some epoxy primer, and then the seam sealer using my finger to smooth it out (dip your finger in soapy water first...it helps the sealer to not stick to your finger).