Here's a comment George. The F in LFNC stands for flexible. I have yet to see any NM cable designed to be flexible. Solid conductors will break after too much flexing.
Regarding the thermostat wire it is a violation to run it inside the conduit with line voltage, however I don't remember seeing any thermostat wire listed as sunlight resistant and suitable for outdoor use. Again the flex problem with solid conductors.
There are a number of "we've always done it that way" things that don't really fit with the Code.
I let the elctricians end their work at the outside disconnect and the HVAC guy can make a mess of the rest of it.
Alan