1) biologically speaking that would mean (eukaryotic case) that you would have a single 'sequence' per chromosome with at each end a telomere sequence and a centormere in the (roughly) middle . In an assembly you'll often miss the telo/centro-meres as those are very repetitive. So for an assembly it's often hard to tell whether or not you have the full chromosome.

2) yes, that is technically possible but holds a certain risk. You can never be sure upfront if your species genome is exactly like the one of the relative. With such an approach you will mimic the situation in the relative to your current assembly, which might be OK in most cases but again you can never be sure of it.