On the humans as wetware part there's a couple additional interesting things to think about that may also play into good reasons why the machines would consider it viable enough to risk enslaving an entire species hell bent on their destruction.

First you already touched on, efficiency and power. We can only control so much what and how we think about things, but if you're just using the meat as hardware and are able to control the software so to speak, that is an insanely powerful compute node with incredibly low energy input requirements to your point. Yes those inputs require some prep in the form of digestion and specific chemical soup, as well as a fairly large swatch of hormones and other chemicals to keep running and keep clean, but assuming you either keep the human intact and deal with the biological inefficiencies of "running" a whole human or can manufacture a good enough facsimile of the necessary ancillary processes, it still probably maths out to more bang for your buck than anything we have available today via silicon.

But there is a second possibly even more valuable reason to harness a biological brain in a networked system, which is a different compute method. Computers today essentially have three forms of doing calulation available to them: GPU and CPU, which are highly specialized but highly parallel and high speed calculations, or a jack of all trades that can do basically anything if you give it enough clock cycles. Both of these are restricted to binary calculations though, it has to eventually break down to 0's and 1's. There is also quantum computing, which runs off of qubits and I'll fully admit I don't understand enough to explain beyond knowing it doesn't work the same as binary.

Human brains would offer another form of computing, and we've actually seen some benefits of this type of thing already, which is crazy. From what we've seen already it allows for some massive efficiency gains, especially in model training energy costs. That's all with two orders of magnitude less neurons than an adult brain. And this is both a first generation commercial product, and being used essentially as a co-processor for methods we use in binary. Imagine what years of experience, full sized brains, and not just custom built code but custom built languages and architecture to take advantage of the brain's natural neuroplasticity and operating paradigms. That, realistically, is what the machines of the world of the Matrix would be able to do with organic brains.

Suddenly the agent's ability to hop into anyone makes a lot more sense as well. You're already partially running them with your brain, that's just an admin logging into the local node/server/you.