The initialization time (from CONF_DONE high to INIT_DONE high) takes more than several tens of ms depending on the ambient temperature. Is it possible for the temperature to cause such a long delay?

It does not take that long depending on temperature.
The INIT_DONE pin requires an external pull-up, but if it is not pulled up or the resistor does not work, INIT_DONE may appear to take longer to go High.

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Category: Programming/Configuration
Tools:-
Device: Cyclone® V