Hierarchical settings do nothing in a flat project.
Think of a flat project as a single sheet, where each sheet in the project is looking at a different section of that overall sheet. There is full visibility between pages. As such, you must annotate the project, because you have duplicate designators on the same single project sheet.
If you're trying to reuse sheets simultaneously in different projects, you will have to make an independent copy for each project, or use hierarchical design.
Sheets called out with hierarchical subsheet symbols can be automatically assigned physical pre/postfix designators, so that R103 becomes R1103, etc. Sheets can also be REPEAT'd for multichannel design, where each channel gets the same prefix, which can be handy for identifying parts on the PCB.
Tim