I would guess the that two black wires in the ceiling are just hot and neutral. The wiring behind the walls may be a bit of a mystery, but as long as you have hot and neutral at the fan, you can accomplish what you want. If you want to put a smart switch at the box for control (maybe a scene controller like the Zooz ZEN32), you can once you find what wires are hot and neutral (assuming that they are available in the box), but you probably don't want it to actually switch the power to the fan in the box.
If your RF remote is working and you are not looking to replace the fan, a Bond bridge is probably your best option. I bought a used/refurbished one on eBay for $50 and it is working great to control my ceiling fan and light. I just set up the wall switch (A Zooz ZEN71) for "smart-bulb" mode so that it never actually switches off power, and I use that switch to control the fan with a single press up/down to turn the fan on and off, a double-click up/down to increase/decrease speed of the fan, and a held button to reverse direction (I use Webcore for the automation, but I am sure you could do the same thing in Rule Machine). I use a button on another scene controller to switch the light on and off. Works great for me.
If you want to replace it, then you have more options. One option is to buy a fan with an RF remote control and use a Bond bridge to control it. If all you want is separate on/off control of the fan and light, you can use a double-relay like a Zooz ZEN52 up at the ceiling fan and then use a scene controller to control the relays. You may also want to look at this:
Looks like it will ship in February. Haven't used it nor researched it but looks promising.
In a previous home, I used a Hampton Bay Zigbee-based ceiling module, but it doesn't look like they are available anymore.