When I was younger I went through a short phase where my phe levels used to come back high one week, and low the next. My dietitian did mention doing my blood test at the same time everytime ie always doing my blood tests right before I go to bed, or right when I wake up. She never mentioned fasting before a blood test, but she did suggest doing it a few hours after I ate.
We decided against doing this, because we did not think it would change much. My levels just straightened themselves out.
As far as breastfeeding goes it could be possible that his phe levels do get a bit higher after breastfeeding him rather than after feeding him his formula. When my sister Erica was a baby my mom breastfed her and she found that her levels came back lower after drinking her formula, and high after breastfeeding. My mom solved this by giving my sister formula and breastmilk at the same time. She used the Supplemental Nursing System (SNS http://www.medelasuction.com/ISBD/breastfeeding/products/nursing.php), but there are other ways you could do this. You could feed him half a bottle at every feeding and breastmilk, rather than alternating formula and breastmilk at every feeding.