A fair few questions in this post. I will break it down as best I can..
Is this syphilis? No. A chancre (the sore which is caused by syph) is more than a red pimple and a divet in the skin. It is an open, often painless ulcer looking thing. Obvious to see. It also appears where the infection took place. You said you wore a condom which protects alot against syphilis but it also means the chancre would appear were the condom wasnt.
Did you test to soon? Yes but in this instance you dont warrant testing unless any symptoms appear. Your little spot was most likly from irritation from the sex or from masturbation but the key thing is, its gone. Chancres last longer than a week anyway.