I think you've included a marked up copy of the manual?, with Mac Preview I can't see the highlighted sections, so this reply is a little blind.

I agree - manual is likely a better system, but with the 30 minutes I spent looking I couldn't find a similar manual-only solution. Hide the remote.

The two switches - one for open, one for close. I'd look to a DPDT centre-off rocker switch (e.g https://www.amazon.co.uk/VASI4KO-Wat.../dp/B004J6PY2A)

That way you can use this single switch to actuate the open in one position, close in the other, and "nothing" with the switch in the centre position.

I don't think push buttons would work well - I think the inputs are non-latching (you'd have to hold the button down for the duration of travel). The rocker switch overcomes this. This applies to the hand-held pendant that you describe.

There are ways around this - without getting clever I'd use two separate 12V relays with diodes in series with the coil - one wired one way, the other reversed, wired across the motor - in one direction one relay actuates, in the other, the second relay actuates, and each relay is used to short the input to the corresponding demand input to the controller. I can sketch a diagram for this later when I'm not getting ready to go to work. But you'd have to understand how the controller behaves if you present two demands at once (e.g. what happens if you press open, when it's traversing to the closed position).

The biggest problem I have with that controller is understanding the connectors required for the manual switches and the potentiometer control. You could do with getting that information to get the switch/speed controller set-up.

Re. the last question - if your issue is the use of 3 wire proximity switches - you can replace these with microswitches for 2-wire interfaces, or use the proximity switch to actuate a relay and use the relay's NO contacts to provide the 2-wire interface to the controller.