If a proposed chiller (or boiler) meets the Tables 6.8.1A-J in 2007 or 2010, when tested with water at AHRI conditions but is designed to be used with glycol for freeze protection, then its actual thermal efficiency may be reduced. 

90.1-2010 Sect 6.4.1.1 Minimum Equipment Efficiencies—Listed Equipment Standard Rating and Operating Conditions appears to address this clearly: "Equipment shown in Tables 6.8.1A through 6.8.1K shall have a minimum performance at the specified rating conditions when tested in accordance with the specified test procedure."

It's unclear from Appendix G, which efficiency to model for the proposed--the derated unit with glycol or the everything's rosy at AHRI conditions efficiency. It does indicate you can enter the standard efficiency if required by the software, but that's not a software limitation here and I think it's geared toward water temperatures and not the working fluid itself. ("Mechanical equipment efficiencies shall be adjusted from actual design conditions to the standard rating conditions specified in Section 6.4.1 if required by the simulation model.")

And which corresponding efficiency should be used in the baseline case? It would seem unfair to model 30% glycol in the proposed and water-only in the baseline chiller. ...obtaining glycol adjusted baseline chiller curves is another challenge.

For reference:

90.1-2007 Sect 6.4.1.2 explicitly avoided chillers using glycol for ice storage or freeze protection with a blanket statement:

"Chillers designed to operate outside of these ranges or applications utilizing fluids or solutions with secondary coolants (e.g., glycol solutions or brines) with a freeze point of 27°F or lower for freeze protection are not covered by this standard."

Addendum bl to 90.1-2007 provided corrections for non-standard AHRI design conditions and potential inclusion to regulate chillers with standard lift temperatures. This strategy was adopted into 2010 Sect 6.4.1.2 albeit with slightly different equations.