I hear what you're saying regarding maching the faces square, however I've rarely seen people mount things that require such accuracy to the spindle mount, so didn't include it in the price. Since the bed of the machine is machined/set to be in the same plane as the machine X&Y axes, then the only inaccuracy introduced would be due to the (lack of) flatness of the material, so the top of the part would be further from square than the other side. However if the customer required greater accuracy, then I would happily add £6 to the price and skim it accurately.

When I make spindle mounts in two parts, such as those for the 80mm spindle, I use the surface plate and height gauge to measure the center height of each mount to ensure they're both within 0.01mm of each other. This is also one of the reasons why the rotating ballnut mounts I've made take a long time to machine - it's important to ensure the shaft is parallel to the mounting face(s), which necessitates careful consideration of the machining order, and accurate alignment...then someone mounts it on bits of welded box section and it's a bit demoralizing!

Anyway, the reason my friend and I can afford to machine this so cheaply is lack of overheads. I just do this to fund my hobby, which is having a workshop. I therefore only charge up to £10/hour and add the cost of materials and postage. If the part is particularly interesting (i.e. complicated, like this one) to machine I charge less per hour. So for the spindle mount, it's about 2.5 hours work plus £5 for the material (@£5.50/kg) and £4 for postage, so 2.5*10+5+4=£34 so I rounded up to £35. I don't charge for CAD as it generally only takes a few minutes and I can do it any time.
If I had to pay rent on the workshop and was doing this as a business, then yes I expect I would have to increase the hourly rate, however at least with having made the machine(s) myself I'm not having to charge lots to pay for the machine.