All of these papers describe competition; that's all they share in common. Competition is ubiquitous in nature; it need not even involve organisms that have ever encountered each other: when you put two organisms together that use some of the same resources, competition occurs. Just because competition occurs does not mean "complex social dominance hierarchies" occur. Just because someone talks about a "hierarchy" it does not mean that hierarchy is the result of a social agreement for weaker individuals to defer to stronger ones to avoid conflict; "hierarchy" just means "we are putting these entities in an ordered list"; the order and meaning of that list depends entirely on the conditions and criteria used to arrange that list. When someone says "hierarchy" or "order" you have to read what they mean by hierarchy/order and not assume that it is related to any other hierarchy you have read about before. If you have some sports teams, you could rank them according to their win/loss record, according to an Elo-based ranking system, according to how much you like their team colors, according to a weighted average of expert/sportswriter opinions about how good the teams are, etc. The teams don't even have to meet each other for most of these measures, they certainly don't need to agree among each other about who is stronger for you to be able to put them in a hierarchy according to your preferred criteria, and even if you think you've designed the best hierarchy possible, their pairwise interactions may not be what your hierarchy predicted.
The type of dominance hierarchy described on Wikipedia is an evolutionarily stable strategy among social animals. In short, by establishing a hierarchy, fighting is limited. Fighting is costly and dangerous: wounds that may seem minor can result in deadly infections, and any effort towards a fight costs energy/calories.
Your question cites several other situations where authors have used "dominance hierarchy" or "pecking order" to describe the results of competition, but not all competition needs to have this social deference-to-established-strength aspect.
With respect to the specific papers you talk about:
This paper is about competition among yeasts. It does involve interference competition and exploitation counter-strategy. However, there is no complex social hierarchy, this is all competition happening on a molecular level. Species/strains that produce and are resistant to a toxin get the benefits of the toxin but also carry the costs of producing it. The authors study a system where growth patches are isolated and from each other and strains spread from patch to patch. When present in the same patch, the toxic strains can often defeat the sensitive strain. However, sensitive strains can be successful in places where the toxin producers are absent, and since they don't need to bother to produce toxins, they grow and spread faster. Depending on the parameters of the environment, the increased growth ability comes into an equilibrium with toxin production.
Nothing social needs to happen for this to occur, none of the yeast strains in these models are behaving in any different way, it's merely a result of the cost-benefit of producing a toxin.
There is absolutely no intraspecies social competition in this paper. They have squid and bacteria that have a symbiotic relationship. If you take the bacteria from one species of squid, it can survive in other squid species, but it doesn't do as well as the bacteria native to that squid, and vice-versa. The closer the squid are phylogenetically, the closer their bacteria are, and the more similar cross-collaborations are better than dissimilar ones. The "hierarchy" here is completely environment-dependent; from the perspective of the bacteria, you have a different hierarchy for each squid species.
In this paper, they study a slime mold that produces a fruiting body to spread. The fruiting body consists of a stalk and spores; in their terms, they call "dominant" strains the ones that produce more of the spores. However, the stalk is important for effective reproduction. Therefore, strains that produce more spores are "cheating" a bit, and this strategy is only effective when other strains are present to make up the stalk. This is a complex interaction, but doesn't rely on any social hierarchy; the "hierarchy" here is simply the ratio of spores to stalk produced by each strain, in other words, the level of "cheating". Being "high" on this hierarchy aka a "cheater" is only good when there are lots of non-cheaters around.
Here they are growing plants together in a plot. They rank these plants according to how they grow in competition with other plants. There is no social interaction here at all. The paper shows how hierarchies can be non-linear due to different demands for resources that appear when different species compete. Therefore, Plant A might outgrow Plant B, and Plant B outgrows Plant C, yet Plant C outgrows Plant A if each are isolated in a bi-culture. Real ecosystems contain more varied conditions than an experimental plot, so in the real world you'll find different niches where each plant exists. Despite using the term "dominance hierarchy" these authors aren't talking about anything but relative abundances in different co-culture scenarios.
The last link is to a book on plants; I won't address it directly here, because it's unclear what part of the book is being referenced, but I am guessing it's describing something similar to the Aarssen article.