Keeping it down to basics, shooting wide-angle underwater the lens needs to focus on the virtual image of the object you wish to photograph. This virtual image is created on the curvature of the dome port. So the lens has to be able to focus on the port - not on the real image which could be metres away.
This then creates two problems:
- will the lens focus closely enough to capture the virtual image?
- given the curvature of the dome, can the lens get enough of that curved image in focus, i.e. can the lens produce sufficient depth of field. Typically wide-angle image edges can be soft as the lens can't get enough depth of field focussing so closely to get the centre and the edges in focus. Most people will shoot at, say, f11 or f16 - but even then there be insufficient depth of field to get the centre and edges in focus. This is especially a problem with FX size sensors and lenses.
Manual or autofocus should not really make much of a difference. It's the close focussing capability of the lens that counts. Often lenses that are superb topside, are not necessarily good underwater.
Hope that helps a bit!