I would advise to stick to what's on your passport. You can always explain a baptismal name, if they ask, provide the baptismal certificate.
However, Names on International passport will usually be the recognized one in this circumstance.
Only PA needs reference letters and education docs. However, depending on your CRS score (if you're close to or above 400) you might want to get yours as well for CIC stage because SINP hsa been rejecting people lately and we don't know your wife's'NOC, education details etc.
(don't put all your eggs in 1 basket)
Good luck!
I really appreciate your response,I will stick with the name on the passport as you advice hopefully the baptismal certificate will help explain it if they ask.
As regard my wife education details she had a degree in microbiology and master's in Environmental biology and public health so we're targeting NOC 2221.