Another way of asking the first question is: are boundaries bad? The answer is no, boundaries are neither inherently bad nor good, per say. Another way of asking the second question is: is the purpose of boundaries to create parts. And here again the answer is no. Part-whole Systems (S) may result from boundary-Distinctions (D), however that is not their purpose.
Boundary-distinctions have to do with identifying specifically what the distinction is and is not and in so doing, consider how that Distinction possibly marginalizes the "other," including other people, opinions, groups, insights, and perspectives. The result of distinguishing boundaries may lead to additional parts, but that is not the goal of Distinction-making. The goal of Distinction-making is to avoid marginalization of other people, groups, insights, and perspectives.
In addition, in real-world natural systems, boundaries just exist. They can be arbitrary but they can also be extremely important and sometimes even protect us. Our skin, for example, is an organ of the body that offers us considerable protections. Thus, the goal is not to get rid of boundaries, the goal is to see boundaries that exist and understand why they exist.
For example part of the COVID crisis involves the boundary-reducing effects of globalization (our interconnectivity (an abundance of relationships) has a decreasing effect on the boundaries that divide us as countries, people, and genetic pools). This makes viruses much more detrimental writ-large because they can readily spread. Because of globalization, boundaries that once existed no longer exist. Boundaries that once protected us no longer protect us.
From a systems lens, we must understand that the positive effects of globalization also have negative and unintended consequences—one of which is the reduction of boundaries and their protections. So, having removed these boundaries from the world-stage, what new and different boundaries must be in place to protect ourselves? When we remove a boundary, we must think about the unintended consequences of that removal. When we add a boundary we must think about the unintended consequences. While there are many many benefits to globalization (e.g., shared ideas, technology, trade, etc.) there are also consequences such as susceptibility to viruses.