By "table-less", do you mean the grid layout, or simply the absense of table code? The default product listing actually is presented as tabular data, so table layout there is appropriate.
If you want non-tabular layout, get the Column Layout Grid mod from Free Addons. Even if you only want one product per row, this will allow you more freedom in element layout. For more control over element positioning, you might want to try Flexible Product Listing (styling product listing pages with column layout grid thread, post 50).
The new products on the home page are not a "listing" but a centerbox, and will not be affected by listing page mods. Centerboxes and the specials listing use non-tabular layout code. The new, featured and all listing pages actually use tables just for layout - I think they are even older code than the default listing.
For most front-end code, the template override system will let you keep your mods safe from being overwritten in an upgrade (you will still need to merge any changed core files that you have overridden into your mod versions manually).
If you are really concerned about your client damaging the site with random admin changes, use the Admin Profiles mod to make him an admin with limited access.