Hi Mark,
That is safe to do. The buffer chips U12, U13, U16 & U17 are what connect to the xDot from the developer card. If they are not powered, they should not draw current. If you are uneasy about that, you can power the developer card with JP5 installed then power the xDot. Either way, configure the xDot IO that connect to U12, U13, U16 & U17 as analog no pull to obtain least power draw. Also pay attention to GPIO0 as it connects to an LED. Again analog no pull would be least power.
Kind regards,
Leon