You'd better make Canadian immigration think you apply for Canadian PR seriously, not just for backup. In that case, you'd better apply with your baby. If medical checkup is the only consern, do not worry about that, there is very mimimum checkup item apply for baby or young child, also, medical checkup usually happen more than one year after you submit your application with current average processing time, your baby is not baby by that time, will be much easier to handle while you bring him/her for checkup.