Yup, seems EPWA is the odd one, however it is not on our route network and not a used alternate, we only fly to one destination in poland. Our SOPs and limits are based on NADP 1 or 2, not the old procedures.
However, VNAV does protect your flap speeds if you fly the commanded VNAV speeds. It commands speeds based on current flap setting and protects even the retraction phase from 1 to up with a 20kts margin (speed will go no higher than 230kts until everything is cleaned up). Indeed the VNAV during takeoff procedure is a boeing suggested one in preparation for the next FMC-Version. In fact VNAV takeoff was already available for the short time 10.8 was around and will be the standard boeing procedure with the next FMC version which is apparently due sometime this summer.
Not using LNAV and VNAV is simply not the way boeing wants the plane to be operated. Of course it is possible, but it is not standard anymore.