From a clinical psychology perspective, this problem occurs across the whole range of psychiatric diagnoses. Every diagnosis has symptoms which overlap to a lesser or greater degree with another diagnosis, which is why so many misdiagnoses occur. And yet two people can be diagnosed with the same disorder without a single common symptom. Schizophrenia and bipolar disorder actually have the highest rate of being misdiagnosed as each other, as there are so many symptoms which can occur in both illnesses. Many people just think that bipolar disorder is only about moods, but it also has a very high occurence of psychotic symptoms as well, as with schizophrenia, and is often treated with drugs which were originally developed for schizohrenia. The system is a crazy one, but I believe it will eventually be changed for something better- a lot of work is being done behind the scenes on this issue right now.
With reference to BPD and PTSD, in my experience most people on psychiatric wards who have BPD (around two thirds of patients on psych wards have a personality disorder) have been abused in some way, usually in childhood. In many people this can affect the ability to form bonds, which can sometimes result in the symptoms of BPD. Then some of these people go on to develop PTSD as a result of the abuse, thus end up with both diagnoses. BPD is not a 'nice' diagnosis to have. These people are often treated by the mental health profession as being manipulative and as troublemakers, and some professionals don't even treat it as a 'proper' psychiatric disorder. Treatment is therefore often inadequate for BPD, although it is slowly improving, at least in the UK. I guess the other issue is that it is estimated that one fifth of the population have a personality disorder, which is another reason why personality disorders are often not treated as illnesses- there is a question mark as to whether 20% of the population can actually be 'ill'.
The other difference between BPD and PTSD is that PTSD definitely has a better long term outcome (on average, of course). Most people eventually recover from PTSD, and it tends to require far fewer inpatient stays than BPD. Once the person with PTSD has recovered, their diagnosis becomes a thing of the past. This is only after a long slog of course, and people may relapse, but most are eventually free of it. Unfortunately with diagnoses like schizophrenia, bipolar disorder, and BPD, the person will carry that diagnosis and illness for life, and will never be free of it.
Hopefully with all the research that is going on at the moment, treatment and the chances of an accurate differential diagnosis will improve. Here's hoping!
Best wishes to all,
KB