Anonymous Guest Poster:
Interesting question. If it would be helpful, I can expand a little on Terrence's "Yes".
It is important to distinguish two different terminologies. Consider the following simple example: X and Z both cause Y. In common SEM parlance, X and Z are exogenous variables. In strict Structural Causal Model (SCM) parlance, their disturbances are the exogenous variables. X and Z are endogenous. This just pushes the problem back a level to their disturbances.
The Causal Markov Condition (CMC) permits the substitution of a shared latent parent for any covariance because it posits that for any covariance there is a corresponding causal structure. Suppose we apply this directly to X and Z, not their disturbances. Once you make this substitution, the covarying variables, X and Z in our example, have a parent and remain orthogonal when conditioning on this parent. So, there is no violation of the Markov Condition in allowing X and Z to covary.
While it is true that Pearl (2009) relies heavily on examples with just one exogenous variable, somewhat obscuring the issue of how to treat multiple exogenous variables, one can find examples. See Figure 4.8 on page 126. X1 and Z are both exogenous but not uncorrelated.
Both the model with the covariance and the model with the latent parent differ both probabilistically and causally from the model with orthogonal exogenous variables. The latter is a much more restricted model (and most likely will not fit your data). However, if one accepts the CMC, then the former two do not differ from one another in any important way. They both represent an unexplained source of covariation among the exogenous variables and among their children. Controlling for the two exogenous variables (e.g., X and Z) screens off their shared parent with respect to their endogenous children (e.g., Y). So, there is no need to model it explicitly.
In the case of your dummy variables, the representation of the patterns of covariance among the dummy variables by pairwise common causes renders the underlying assignment mechanism a little obscure to the eye. However, it is an acceptable representation for purposes of statistical analysis. You are not violating any assumptions by adding covariances between exogenous variables in a SEM model.
Caveat: What I am describing is the canonical interpretation of SCM. I am not necessarily endorsing the uncritical acceptance of that interpretation or of the CMC.
I hope that helps,
Keith
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Keith A. Markus
John Jay College of Criminal Justice, CUNY
http://jjcweb.jjay.cuny.edu/kmarkusFrontiers of Test Validity Theory: Measurement, Causation and Meaning.
http://www.routledge.com/books/details/9781841692203/