Background Pony #6522
Okay, bear with me here, sun is getting up here, so it might be hard to read what I'm saying, but:
What if the sun was controlled by Celestia and Twilight specifically? What if this is some sort of magic that got lost? As is; they have far weaker control of it now then they had before. As far as we seen, there is no actual source of knowledge about sun/moon magic other then Celestia/Luna, and then Twilight. Seeing how this is a thing, I could see said control getting weaker and weaker over time, as knowledge that is shared orally tends to mutate hard. (Maybe particular alicorn is not fan of weather magic, studies about it less, then gives that 'smaller' knowledge to his heir, who in turn, whist being okay mage, is not so great to replace parts of magic that got lost, and so forth down the line, with it getting weaker and weaker.)
We have definitely seen magic knowledge getting lost in the past, so this doesn't sound like too much of a stretch for me.