Engineers will always need public input to make sure that their design requirements meet the public's goals. There are a variety of ways to collect that input; some are fairer than others, and some are more politicized than others. Bicyclist advocates need to participate if they want to see their interests represented as strongly as the local neighborhood intersts, the business interests, the highway department interests, etc.
Usually the engineers ignore cycling, or include a token mention of some standard treatment that they might implement without thinking about it. Speaking up gets the engineers to pay more attention. In some cases, however, the engineers just plain screw up, and it needs to be called out, in engineering terms if necessary to make the point. As long as the feedback is done respectfully, constructively and transparently, the engineers are unlikely to retalliate, and are much more likely to adjust their game appropriately to a raising of the bar.