All perfect praise be to Allaah, The Lord of the Worlds. I testify that there is none worthy of worship except Allaah, and that Muhammad is His slave and Messenger.
There is no comparison between the Christians' claim that 'Eesa is the son of Allaah The Almighty and the Muslims' saying, "May the prayer of Allaah be upon Prophet Muhammad ," or any other prophet. Anyone who compares them does not know the meaning. Despite the Christians' saying and belief that 'Eesaa is the son of Allaah, Allaah The Almighty is above all such claims. It seems naïve and contradictory to their belief that he was killed and crucified and therefore a sound mind cannot accept it.
On the other hand, the Muslims saying, "May the prayer of Allaah be upon Prophet Muhammad ", is not in fact asking for prayers but merely a way of asking Allaah The Almighty to bless, have mercy upon and increase goodness for the Prophet .
Moreover, it refers to the fact that Allaah The Almighty mentions him among His angels in the heavens. That is because the Arabic equivalent of the word 'prayer' encompasses all these meanings. Having known this fact, comparing the two statements is totally irrelevant.
Allaah Knows best.