Hi @stat_mr_h,
It seems your response Y2 could be some kind of indicators/price response.
Your design is built independantly of the responses, the design structure depends on your objectives, the factors (factors type, number of levels...), expected modeling complexity (assumed model), and a compromise between experimental budget and precision in the estimation of effects (aliasing structure, number of runs, replicate runs, ...).
You could build a model for response Y1, use the prediction formula Y1 and theoritical formula response Y2 in the Profiler to try to optimize both responses.
As an example on dataset "Bounce Data" with the response "Stretch", I added a column "Price" with a defined equation:

Once a model build on response "Stretch" (Y1), I save the Stretch Prediction formula and Launch the Prediction Profiler Platform with the two formula (predicted Stretch formula and the one calculated for Price in the datatable) to optimize both responses :

This would be the first approach you mention. As you already know the formula for Y2, it doesn't make sense to try to model it.
It's not a problem of multicollinearity, as each coefficient could be determined independantly and precisely (without errors) with the design used (VIF = 1 and Std error = 0):

Hope this response will help you,
Victor GUILLER
"It is not unusual for a well-designed experiment to analyze itself" (Box, Hunter and Hunter)