Will a transmission check engine light cause my car to fail emissions in Illinois?

2001 Lexus IS300, first had a code for a faulty Automatic Transmission Fluid Temperature Sensor, changed that with a drain and fill of the fluid. Now the CEL is on for a faulty input turbine...something. Technician pretty much said vehicle needs a new (or replacement) transmission. Now, transmissions have nothing to do with emissions, but the CEL is on because of it, will this cause me to fail the OBDII test? I don't live in Chicago, I go to the test facility in Naperville, IL Thank you.