No, they auto-tune during each startup/reboot. Been that way for many batches now.
This is simply not true! They run the autotune routine ONLY on first start or after a hard reset (possibly on other rare occasions), but definitely not after every restart be it clean or unclean. There is a flag set in the filesystem that triggers the autotune routine. Maybe somebody could point out where it is exactly - cannot remember off the top of my head. Source: Operating S9-13.5TH/s miner.
It seems as though you have a major misconception about what the auto-frequency is and how it works. "Autotune" is an uniformed, social-media contrived name based on too many misconceptions of what happens in the process. When it comes to "newer" models of S9s, auto-frequency has a specific frequency set for each chip. This frequency is set in the PIC, and this setting is done prior to shipping to the consumer.