Better support for rio methods such as clip/reproject when parse_coordinates=False

[snowman2]

Currently they just don't work. When the coordinates don't exist or aren't defined, they are auto-generated incorrectly.

Issue: recalc=True is default in transform. This can cause incorrect results. Need to find a way to detect this and return the cached instead.

rio.clip_box - potentially use from_bounds with rio.isel_window.