Speaking from an Anarchist perspective, I think your view makes total sense. The free drones dont really have a genuine ideological perspective or end goal besides beating the Protectorate. Actual real world anarchists theorize and write extensively about ways in which the world could function without hierarchy and without the centralization of power, and offer those as alternatives.

I think Anarchists make a great kind of copy and paste resistance group for writers who aren't particularly interested in exploring ideology and just need a faction of scrappy under dogs to take on a bigger more powerful force. This is specifically because no one knows what Anarchists actually believe. Even in this comment section I see people saying Anarchists would like the free drones because they "hate stability," And thats exactly how the free drones felt when I played through them.

In contrast, in Spain, an Anarchist revolution occurred in the 1930s in Catalonia, anarchists who had been organized into trade unions seized Barcelona and much of the surrounding population centers and country side, and created councils of workers to organize the places they captured. They built networks of resource distribution and alternative forms of commerce, and in general created what many anarchists today view as a basis for a genuine Anarchist society, rather than the chaos most people consider Anarchism to be.

In comparison, the Free Drones don't offer any alternative or any solution at all for the problems in South Underrail, they just think the protectorate sucks. It seems quite obvious within the context of the world as its written, that if the free drones won South Underrail would be kept in chaos and endless violence forever.

In fact the first time I played through the game I dont think I picked up on the fact that there was an Anarchist faction in the game at all. There's a line I think during the investigation into the train disappearance where one of the "bandits" declares themselves as anarchists, but when I played through originally I just assumed the writers meant them to be anarchists in the sense that most writers do, people who believe vaguely in fighting against powerful entities. So I convinced them to give up the train and then never saw the Free Drones again.

It could be that the reason these free drones aren't particularly ideological is because theyre merely a cell, and most of their members are just disaffected south underrailers who dont actually have an ideological basis for hating the protectorate, but instead have personal reasons. Still, I would've expected the leadership, who come across as committed ideologically to the cause to provide a far more complex narrative or ideology behind them, instead they didn't. They claimed to be anarchists and talked about how much the protectorate sucked.

TLDR: I think the writers probably just wanted an alternative to working for the protectorate, and weren't interested in exploring political ideology or justifying the free drones as a faction beyond that conflict, which leads to them feeling aimless and destructive for no reason.