I'm not sure about right and wrong, but I don't think your time dependency is required to use covariates. Only that you can take a measure of the covariate for each treatment. Also I don't think I understand your Use of this Variable statement. The covariate is a random variable in an otherwise fixed effects model. Thus you have a mixed model. Accounting for the covariate reduces the MSE estimate (if this was not accounted for, the MSE would include the effect of the covariate). One could argue this increases the precision of the experiment. As a random variable, I typically start with adding the first order effect, but there may be additional effects you can estimate (interactions and non-linear). If the covariate is indeed significant, the user may be able to input the covariate value in the model and solve for remaining significant factors (elect levels) in the model to improve the results.
I am always interested in determining causal relationships. It is our hope (wish) that we can develop a useful model using factors that we are willing to manage, but that is not required of nature. It may be in the noise which is extremely useful to the practitioner. Knowing the significant variation is from noise leads one to broaden their investigation. One may find they are willing to manage factors they previously did not or one may desire to become robust to the noise both choices are important to the practitioner.
"All models are wrong, some are useful" G.E.P. Box