In most cases the version from dns_soa_list.php can be used as it does not require to create a new object. But sometimes it is nescessary to create a new object to override subfunctions, in that case the version from web_domain_list.php is better. Both versions have the same functionality, so I dont thint that its nescessary to edit the existing files.
Sounds good. Maybe you could consider removing some headlines in the sites module menu by combining some pages. There are so many cats with just one site. For smaller resolutions height is very limited. I often forget that not all users have displays with a 2560x1440 resolution.
I add a feature request for that in the bugtracker.