There are many good points here. I agree with your previous article with which you link, that the idea of NGO-led development should change. To be overly broad-brushed, NGOs really took off when the state in developing countries was being pruned back by fairly neoliberal ideas, enforced by structural adjustment and the crumbling of one type of state-led planning and development. They were the 'third way,' where states and markets couldn't or didn't function for whatever reasons and to that end, they have done a lot of good in a lot of lives.
What I point out above doesn't mean that NGOs were complicit in a neoliberal philosophy or attempts to undermine the state but it does mean that their role has often been to substitute for the state and its capacity. Ultimately, this limits citizens' rights to have real conversations (via elections and other means of grievance redressal) about the social compact and what is owed to people by a government (and in return for what; I obviously do not advocate for the rentier state no matter what public goods they deliver, nor I am excluding the possibility of states and markets working together or the market delivering some goods/services on its own).
NGOs may plug holes where there are government or market failures but my sense is that they should be a temporary fix, drawing attention to a problem, getting it on the agenda, and showing that there are viable solutions. As you suggest, they can be innovators and incubators of radical (and practical) ideas but, like many tech start-ups, perhaps the goal should be to be "bought up" either by a firm or by the government. Maybe scale should not be the goal. Rather, NGOs take risks that governments cannot and pave the way for the government (or, again, the private sector) to try new things with less risk.
Do things work perfectly when lumbering bureaucracies take up the ideas of nimble and passionate organizations? No, and that is a major challenge that students of organizational behavior will need to take up.
Of course, many NGOs have the mantra that they are working to put themselves out of a job. But their actions and grant-seeking do not always align with their words.
Peter Evans writes about the "developmental state" and the symbiotic relationship that governments and markets should have with each other. It may be time to revisit this idea and discuss where the 'third sector' fits in in different forms of the developmental state, what kind of symbiosis works and what kind instead lets governments off the hook.
It is precisely for the 5 reasons that you list about NGO sustainability that we should think seriously about whether NGOs (or, worse, charities) are a long-term solution to ensuring human capabilities / equality of opportunity are fulfilled, which I think is a goal on which most people can agree.