Realistically, it's entirely possible to bootstrap without going full GmbH right away as long as you can do it quickly. There's a grace period where you can retroactively designate stuff to fall under the GmbH you created later and if you are smart about it, you can move your software project into the GmbH if it's plausible that it was created during that period.
In other words: you don't need a GmbH to build a prototype but it's probably a good idea to have the GmbH in place before you're production ready. Also people are way too squeamish about UGs (micro-GmbHs): they're actually fairly normal in the startup space and end users don't care about that distinction and larger companies are more interested in knowing you have sufficient capital/insurance to cover any liability claims rather than what it says on your letterhead - a full GmbH isn't worth anything to them either because they know you can literally buy and repurpose a shell GmbH for cheap.
I agree that a GmbH is not necessary if you don't consider VC investment an early/eventual goal for your product. If you can bootstrap and build a sustainable product, the biggest advantage is that having a GmbH (or UG) makes it easier to appear as a serious business but as you say, often e.K. is another viable route for that. And as you say, the managing director of a GmbH is still personally liable for anything that could be considered a neglect of their legal duties. Plus the way most people found GmbHs, the owner(s) are usually €12.5k in debt to the company as you only need to transfer €12.5k of the €25k initial capital directly to the company's bank account.
That said, things get messy if you're in GbR territory, i.e. if you have a co-founder who is a co-owner. You can approximate something of a worker cooperative by having everyone individually be an Einzelunternehmen but then you'll have to structure your business in such a way to still split profits fairly while also avoiding running afoul of Scheinselbstständigkeit (fake self-employment) - there's a good example in the Premium Kollektiv[0] (and plenty of literature and research articles have been written about their approach) but this is more of a case of "bending the law" and not something the law was written to explicitly support. A GmbH has the advantage of being structured in such a way you can precisely define split ownership but the disadvantage is that by default this will mean your co-founder can just decide to quit and still retain their ownership because the ownership and the job are legally distinct concepts.
Lastly an often overlooked caveat of GmbHs (although this in part also goes for all self-employment) is that German laws are written with the idea that "business owners" have access to generational wealth and are thus exempt from many aspects of the welfare state and this is even reflected in times of crisis: there were for example COVID relief programmes for solo-entrepreneurs (including solo GmbH owners with no employees) as well as COVID relief measures to allow downscaling employee hours (and thus costs) but if you were a small GmbH with more than one owner, most programmes were not available to you. Things also get nasty if you're a woman who wants to have children while owning (or co-owning) a GmbH: legally the best option for heterosexual couples looking to start a business is still for the woman to be an employee (no, not a managing director either) and own zero shares in the company and even then the German IRS may decide that the woman has a controlling influence and retroactively reclassify her as a co-owner. In short: if you're an entrepreneur in Germany, either don't be a woman or plan to abandon your company in favor of dependent employment if you try to get pregnant.
[0]: https://premium-kollektiv.de/