W&S-139: A Seller could execute the REC Contract with all three utilities (AIC, ComEd, and MEC). Given that ComEd is in PJM, for which the REC tracking system is PJM EIS GATS, while AIC and MEC are in MISO, for which the tracking system is M-RETS, does that mean a Project has to be registered in both GATS and M-RETS for purposes of delivering the RECs?

No. Each utility has an account with both PJM EIS GATS and M-RETS.  Thus, any one Project only needs to be registered with either PJM EIS GATS or M-RETS, but NOT both.  The Seller can transfer RECs from its account to each of the utilities either from PJM EIS GATS or from M-RETS.