Can DNA fingerprinting tell you if someone has been genetically engineered?
Could the technicians/scientists who perform the DNA fingerprinting procedure for the FBI be able to tell that this man is different from other humans?

If by different you mean genetically engineered, it depends on whether the loci tested have been engineered to such an extent that they are substantially different from other humans in order to arouse some kind of suspicion. There are other tests could be done that would show, at the least, that this individual's genome is abnormal.

Would it be possible for someone to be human and have a different number of chromosomes?

Yes, this is called aneuploidy and is the cause of many genetic disorders. Fingerprinting would not detect this.

Does all DNA fingerprinting appear as bar codes and mean nothing until compared to a sample?

DNA fingerprinting looks at sequence length polymorphisms and essentially tells you the length of certain regions of DNA in an individual. In fingerprinting, samples are compared to see whether DNA from two samples come from the same individual. A single sample obviously wouldn't work for this, but that doesn't mean it would tell you nothing.