Optimise SVG

No. Everything removed is invisible to a renderer: comments, the XML declaration, editor namespaces from Illustrator, Figma and Inkscape, empty groups, duplicate attributes, and coordinates written to more decimal places than the file's own scale can show.

An SVG is markup, and a browser runs the script inside one. A file with an onload handler or a remote image reference is a file that executes code or reports back when someone opens it. Since an SVG optimiser is usually the last step before a file goes onto a website, removing that is not optional, and the tool tells you when it has done so.

Yes. References that point inside the same document, which is how gradients, clip paths, masks and <use> work, are all kept, and a group carrying an id is never removed even when it looks empty. Only references that reach outside the file are dropped.