Periodic Calibration enables the Atheros chipset to determine the current average Noise Floor level and also the (genuine wireless) signal levels on the channel, which in turns allows it to correctly set the Adaptive Noise Immunity system (if enabled), it also assists with calibrating a correct IQ balance for the multiple streams, sets the receiver's AGC levels and the A-to-D conversion gains.
This is a hardware and very low level function of the Atheros Chipset and MikroTik will therefore have very little control (and quite possibly none at all!) over how it works, especially as it is also covered by an
Atheros Patent and also an NDA. As far as I have been able to determine in the past when I researched this, there are a number of different values that are made visible by Atheros to developers in the API calls besides the ability to turn on/off the ANI function, how frequently to request it performs this calibration (default is 60 secs) and an ability to extract the long term / rolling average Noise Floor measurement obtained by the hardware. However, whether MikroTik uses any or all of these API calls or the values they return is obviously pure speculation.
Therefore, in answer to your questions more specifically:
Q. Should periodic calibration be setup on AP or CPE?
A. It will use the value entered as soon as you enable ANI and will apply to either mode.
Q. During each interval, will CPE experience any packet loss?
A. If the channel is very busy, it may not be possible to complete a calibration measurement in time. How MikroTik RouterOS handles this problem is unknown. I am "guessing" that the default 60 second period is long enough to ensure that there are not too many calibrations so as to be noticeable to any packet loss.
Q Our APs run in AP Bridge mode, is it compatible?
A Yes
Q Are the default settings for periodic calibration sufficient?
A Yes. However, MikroTik provides you the possibility of lowering or raising the value to suit your particular situation. But the default should work just fine. I have not personally seen much difference in performance by varying these default settings. But as the saying goes - YMMV. (Your Mileage May Vary)