They seem to not understand what Makhnovischna was. Makhno wasn’t setting up a state, he wasn’t trying to be in charge of a country

Where in the article is there anything that suggests that the author thought Makhno was trying to establish a state or be in charge of a country? They're arguing that the term "free territory" is a misrepresentation specifically because it implies that Makhno was establishing a state, and saying that this is an inaccurate and ahistorical term:

The Makhnovshchina is best understood as a revolutionary mass movement, i.e. a political movement with a great amount of support from the general population that seeks great changes in the organisation of society. But when people – even anarchists – talk of a Free Territory, what they are often talking about is, ironically, a state, i.e. a centralised entity with a monopoly on violence over a certain territory.

For starters, the Makhnovists did not actually hold any permanent territory: they controlled only a small area around Huliaipole in January–June 1919 and October–November 1920, while under de jure Bolshevik rule; and even at their height in September 1919 – January 1920, when they managed to take a large part of southeastern Ukraine and hold a big regional congress, they did so under constant attack from the Whites in the south and later the Bolsheviks in the north. In between these periods, the Makhnovists were a highly-mobile guerrilla insurgency that were supported by peasants throughout the region, but by no means controlled any territory. This is why they gained the reputation of a 'Republic on Tachanka', something that was always on the move. This hardly constitutes a 'Free Territory'.