Assuming that your model is correct, then the R square metric estimates the proportion of the variability in Y that is associated with the variation in X.
The process variation and the measurement variation are inseparable unless you perform a study that varies both of these sources of variation.
You have the 'fixed effect' of X and you have the 'random effect' of the process and measurement. The random effect can be decomposed further with a properly designed study and analysis.