Sure Scintilla functionality will work with multiple selections, but possibly I'm not being clear, I am talking about Geany functionality that is not built into Scintilla, it will not know about multiple selects/cursors and will only operate on the main selection. And at the moment most Geany functions do not work with rectangular selections, only the functions that happen in Scintilla work AFAICT.
And the same applies to functionality provided by plugins, both core or Geany-plugins.