The chirping noises from the engine compartment is made by the fuel injection system that's running on extremely high pressure just like any other car that has a Direct Injection system, and sometimes there are unfamiliar noises like this, when things are not your common port-injected engine as in traditional cars.
It has nothing to do with the transmission, or the choices you make on which transmission you choose.
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Moto Miwa
R&D Driving Engineer, Product Designs
Consulting for Cusco, OEM+, RS-R, Toyota Japan, and Unplugged Performance.