User switches to another (non-Scintilla) application and copies some other text from it User returns back to Geany and performs a paste. Scintilla remembers it did a block copy in (1) and will paste this text in the block mode even though the clipboard contains something else now
No it won't, the other application advertising new clipboard contents won't offer the "SCINTILLARECTANGLE" target (unless its another Scintilla which copied in rectangle mode), so Scintilla won't paste as a rectangle.