Just downloaded the game today after seeing the post on Tumblr, and I like it quite a lot, though I'm finding it hard to get used to the default mouse setup. Is there some way to invert the Y-axis, or are there plans to add such an option alongside the "Always Run" toggle?

I'm not at home to test this, but I'm pretty certain the vertical axes are bindable in the input menu. You might be able to flip them there

It does not appear that they are, sadly. There are "horizontal" and "vertical" controls listed, but they are for the movement controls and not for looking - looking controls, meanwhile, seem to be completely absent from the list.