Margulis described eukaryotes as aerobic organisms thriving under toxic conditions. And bacteria, that are mostly anaerobic, were by her given the honor of creating an advanced aerobic form, the eukaryote. But there are also anaerobic eukaryotes. These are with the endosymbiosis hypothesis posited to have been reverse evolved by loosing all the features that were needed for aerobic respiration, and instead new features for use under anoxic conditions were constructed. The results of this evolution were organelles like the hydrogenosomes and the mitosomes.
With OET these organelles were created at an early stage of evolution. The mitochondrion and the chloroplast represents the terminal stage of evolution, not any start of reverse evolution. OET holds that anaerobic eukaryotes are ancient, not recent forms. And that is also consistent with the phylogenetic studies that have been performed, if they are interpreted correctly.
With the endosymbiosis hypothesis we could wonder why there are anaerobic eukaryotes at all. But people, when they have been used to the endosymbiosis hypothesis, are also used to events that are almost impossible. The prevailing conditions any place where there is light is the oxic condition. And light is needed for energy generation. The anaerobic eukaryotes are therefore found only where there is no access for oxygen and where thee is a constant supply of metabolites. Typical places are in the ground and in the stomach of cows and termites. They must be older than the animals, so they must have thrived in the ground. With OET they have remained where oxygen has not got access. With the endosymbiosis hypothesis they must have had a lot of problems moving from oxic conditions to anoxic while their metabolism has been reduced and then reinvented in another direction, a direction that was based on cooperation with certain methanogen archaebacteria. And in these habitats they would have to compete with bacteria, that were well established.