Screw and washer should go through flat area or curved?
The depression you're asking about appears to be simply sloppy manufacturing to me. It doesn't seem like an intentional countersink. If it was you'd probably have flat-head screws instead.  


The washer goes under the nut when working with metal, not under the screw head (unless there is no nut or it's an integrated nut). 
The screw head should be oriented where it's accessible and gives the best appearance. 


I'd put that ugly dent against the mounting surface and the screw head against a nice flat hole, personally, No matter where you put it you'll mash that tubing if you tighten too much, so go easy.