color of seam sealer?does it matter?

Color shouldn't matter. It's usually top coated anyway. It is not bad idea to epoxy prime your seams before applying the sealer too. Factory didn't do this but if the sealer fails, you still have some protection.

I've used urethane seam sealers but not the product you noted. The difference appears to be mode of application. A brushable seam sealer would work just fine too and probably be less expensive than the 3M. Just stay away from 3M Fast 'n Firm which comes in a caulk tube. It is ancient tech and if/when it cures, tends to crack.