He was registered as Prince which may have needed both parents to be present at the registration. The birth cert would show for sure.
Sarah Prince died sept qtr 1865 aged 25 and Emmanuel remarried to Harriet Jenkins dec qtr 1868
I'd wondered if there was some split from his father but there's a death registered Cardiff for Emanuel Prince aged 60 in march qtr 1901 and he's living in Penarth on the 1891 census with Harriet and children.
I have a relative using his stepfather's name on one census although children's births are registered with their real surname. No idea why!

Yeah I just discovered Emmanuel's second marriage. They're living together in 1871 at least, after Sarah died. I've had ancestors turfed out at young ages after their parent remarried.
I need to stop digging now because I told them I'd write up a little summary for tomorrow, but I'm only on one branch so far. It's quite refreshing having an entire new tree to build!