Yes the bottom row will have the same key spacing but you can put any key you want in each space – the spacing is 1.5U 1 1.5 space bar 1.5 1 1.5 for the bottom row for all variations.  By default, if you choose the HHKB-like layout, the Ctrl and Caps Lock keys will be switched from the regular Model M layout so they are more in the layout of the HHKB.