You should think very hard before disregarding any recommended non-normal Boeing procedure. You may not be fully aware of the implications. I am not familiar with the B727 systems, but as for recommended medium flap settings, this may be because of inability to raise the gear and go-around implications. Under failure circumstances, you are operating outside your usual mode, and as for disregading advice contained within the QRH, I would suggest not! There are circumstances where maybe you would be restricted at a particular airfield only with wheels down and unable to divert where it may be a consideration to land above crosswind limits, but in a simulator scenario, you really should not disregard such advice as it may be good information about connected problems you may not be aware of.