So long as it is neatly rendered, I wouldn't worry about it, Nick. It'll honestly look fine. If anything, it could have been a lot worse as the roof is flat and not pitched.
When it comes around to rendering/painting, it looks like he can remove and replace one of your panels but not the other as it has some climbers on it. I wouldn't give consent for removing that panel as it'll damage your plants. He should be able to paint/render behind it easy enough if he has the other panel out.
Given that you're the one who looks at the wall, I'd have a word with him and ask if he minds if you keep the visible wall neatly painted every so often just so it doesn't discolour etc. Only takes a few passes with some white masonry paint once in a while. You could ask him which brand/colour was used and get the same type.
Also, your call on the fence panel/planning permission thing but I'd be tempted to put it in on the sly. The other thing you could do, which might be a way around it, is to attach a trellis to the top of your fence. My brother did something similar for a customer:
Get a couple of clematises or honeysuckles and you'll barely see it once grown.