That's part of the Body in White (BIW) of the car.  Typically, it's stamped and welded together on a jig by robots and not manually welded.  The "clay" you see is also not clay but some type of epoxy which is commonly used in joints of sheets for cars (even BMW's here) .  Honda should be very stringent on the specs of the BIW for their cars and it's all based on automated manufacturing process.

Here is a pic of the BIW for the 2016 Civic.  See how stringent Honda is in using different materials in the BIW for safety and ridgity purposes.

Just collected my wife's Civic 1.8S Lunar Silver this evening.

I drove about 50km in total since. My brief observations:

1) The 1.8 CVT is NOT sluggish at all. A complete difference to the City and its slight more powerful than the HRV. I think its been tuned to suit the Civic.
2) NVH is good and gives you the conti feel. But Honda should have done a better job with the NVH between the engine compartment and the cabin.
3) The CVT gets loud when you floor the pedal during hard acceleration but very quiet when cruising
3) Tyre noise is there probably due to Conti MC5 tyres (which are just medium range)
4) Fabric seats are sufficiently comfortable but I would take leather anytime
5) Seats are well designed and suits body contours well.
6) Steering feels firm when cruising and light when manoeuvring. Honda did an excellent job here.
7) Brakes are good and gives you that extra confidence
8) Aircon is damn cold. I usually have the temp set at around 19 deg in my own car but in the Civic I had it at 24 deg.
9) Suspension is a bit on the firm side but makes cornering good

Really satisfied with the 1.8S. I was preparing myself for a sluggish ride especially since I drive a F10 myself. But kudos to Honda for doing a good job in minimising the negative effects of the CVT.