Is there a way to control the order of appearance of shipping methods in Craft Commerce?
I don't think there is any in-built way to do this, no.
A relatively easy hack to achieve it, though, is to loop through your shipping methods (as youare) - but rather than directly outputting them, instead add the data to a twig array (possibly adding some extra data long the way, such as a sortOrder of your choosing, based on the handle) - and then use Twig's sort to sort your options based on your desired criteria (e.g. the aformentioned sortOrder or just by e.g. the price - before then actually outputting those options from the array, rather than the initial direct loop.
It's not awesome/elegant, but it works!