On a hunch I checked a few later WNW kits and sure enough, the same wording is used, particularly where lozenge camo is used (Fokker D.VII, Hannover, etc.). Go back a few releases and mention is made to apply over gloss but no comment about not using clear. The earliest kits, such as the LVG, make no mention of gloss at all.
So, it's not specific to the W.12. Still odd that they'd warn not to use clear gloss under the lozenge yet make no indication as to what color should be used.
Eric