Altium: Change part designator from Letters to numbers
You can do this via Tools -> Board Level Annotate.

You will need to select $ComponentPrefix$GlobalIndex in the "Annotate Options" screen. 

However, this is uncommon for Altium and "Copy room format" might behave erratically, so I wouldn't recommend it.

You can always set custom designators for your physical components. To do this, you will need to compile your schematic (c->r) and in the bottom of your schematic you will then see the name of your compiled sheet, eg. U_IO1, U_IO2, ... Switch to one specific sheet and then double click the designator. This will give you the "Physical Component Properties" screen where you can assign a designator manually as well. Again, not really recommended.