Willit Run, you have identified an important difference between LRC and CI - the inclusion of wind. There are some LRC data sets that have values for different winds.
As for "biasing" for a particular aircraft, this is what PDA does.
As for route specific adjustments, this can be done based on fuel costs and then on a day-of-flight basis if there are specific constraints such as arrival time requirements. Again the caution here is using the right tools to adjust CI and flight profile to achieve an arrival time; slow down to arrive after a morning curfew or arrive before a night curfew, needs to be tempered with what is really possible. This is a complex discussion that really needs a number of graphs and data sets to illustrate. Unfortunately, very difficult to accomplish on a forum.
One of the other issues associated with this is the "planned" departure times and block times in an airline schedule. If not done properly this can lead to far to many operations requiring tactical speed adjustments. The challenge is that block/departure times are hugely influenced by commercial constraints to gain a competitive advantage when attracting customers. Many travel booking engines rank by departure/arrival time and this influences customer choice. Having participated in these discussions it is fascinating.....