Here are my thoughts (though you may disagree and decide to ignore them):
I first want to address the repeat measures. Repeats (or within treatment measures) are used for 2 purposes:
1. Increase the precision of design without negatively restricting the inference space. Averaging reduces the short-term noise component and therefore increases the precision of the design (e.g., measurement errors, within part, within batch, etc). Before you summarize the data you should assess the variability. Is an average an appropriate statistic? Graphical techniques may be very useful. Looking at the distribution may help, but it can also hide time series effects. You might want to assess how consistent the variation in the repeats are across the treatments (perhaps range charts).
2. If your problem is a variation problem, not a mean problem, then the appropriate response variable must be a measure of variability. Repeats enable you to get an estimate of the variation within treatment (e.g., range, standard deviation, variance). Using measure of dispersion as a response variable when analyzing the experiment will help to understand factor effects on variation. Again the nature of the data should be evaluated before determining the appropriate enumerative statistic.
With respect to prediction equations and associated confidence intervals. Extrapolation of the results of an experiment is an engineering or managerial decision, not a statistical one. The confidence intervals in your plot are for the data in hand and could have nothing to do with what you will get. What determines the usefulness and effectiveness of the model you create as a result of the analysis of the data in hand depends on how representative the data in hand is of future conditions. This is greatly impacted by how noise was handled during the experiment (noise in the inference space and noise that was changing during the experiment).
“Analysis of variance, t-test, confidence intervals, and other statistical techniques taught in the books, however interesting, are inappropriate because they provide no basis for prediction and because they bury the information contained in the order of production. Most if not all computer packages for analysis of data, as they are called, provide flagrant examples of inefficiency.”
Deming, W. Edwards (1975), On Probability As a Basis For Action. The American Statistician, 29(4), 1975, p. 146-152
There is no answer to your question as to which approaches are "correct". There are multiple ways to develop prediction equations that take into account uncertainty in the future. Each of has their own experiences and biases as to which method is most useful/effective, but I have found the methodology I use is situation dependent. No one knows the right one á priori. Try multiple methods and then run the process and assess which model is appropriate. Your focus should be on the data collection process rather than on a technique in the data analysis process.
"All models are wrong, some are useful" G.E.P. Box