The Boeing issued flight crew training manual for the 737-6,7,8,9 and BBJ does not allude anywhere to the flaps being lowered during a reject...
No it doesn't with standard Boeing. But the FO selecting flap 40 used to be a recall item for the evacuation checklist with standard Boeing. I believe however, that different operators can have their own procedures approved which may vary greatly from the standard stuff.
I just took a look at the Smartcockit stuff. The Ryanair reject manouvre alludes the outdated procedure of the FO flap 40 recall item on the old Boeing evac checklist. It is dated 2008 when the standard SOPs changed and maybe Ryanair have also amended their procedure since then?