Don't get me wrong, I sold a nice (to me, anyway!) 650 Triumph Bobber before Xmas and have a half-built unit bobber project in the garage currently, but there's no denying quality of home-built bikes can vary widely, and for every "very well engineered" bike there's another two only worthy of breaking for spares.
Poorly mounted seats, badly engineered brakes, piss-poor electrics, tight cables, exposed chains, etc etc are all common faults, and no-one (unless you hit a real mug!) is going to pay the going rate for anything like that.
Build what you want, and good luck to you, but you're unlikely to get your money back (well, unless you build it chicken-sh*t style for five hunderd quid).
Had to laugh recently where someone (on the Dirty Bobbers forum) was going to take a bog-standard and running Daytona and bob it, and some other toss-pot egged him on by saying a good Bob would be worth seven grand easy....
Not in this world, old pal....