Is there any case using atlas is not the best idea?..
when to use a material/texture per object?
Simple answer: if they don’t share the same shader, or if they aren’t going to be loaded at the same time (in the same scene).
I wouldn’t attempt atlasing tiling textures either.
On one project, we encountered a case where very few of our items had emissive details, resulting in huge black maps with tiny lumps of colour. That wasn’t great…
I guess you’ll want to pack together objects who share roughly the same characteristics.