Optical quality deteriorates on long focal length with variable ND filter

Possibly, but if the body has IBIS it should handle that just fine.

I would

  1. wait for a sunny day, without wind,
  2. find a subject far away,
  3. get an ND filter so that I get 1/1000s or so at maximum aperture the lens supports at 300mm,
  4. and start taking photos (JPEGs are fine), decreasing the aperture until I get down to the minimum and eyeball the images. Eg going from f/5.6 to f/22 is a factor of 4^2 = 16. Repeat with and without IBIS.

If, at any point I start getting blur, I would know that it is not the ND filter (because that did not change), and would see if IBIS is a culprit or not.

If there is no blur at this point, dial in the ND filter to get the shutter speed of the last image at the widest aperture and repeat step (4).

At some point you will get blur, and you will know the culprit.

On my Fujifilm X-T4 I have to deactivate sensor IBIS because it creates evident artifacts by compensating non-existent movements (on a tripod).

Also, I have a long focal length, and even if my tripod is supposed to be able to handle that weight I can observe a slow drift during long exposure due to the high torque. This is especially the case in portrait mode and because the lens does not have a mount for the tripod.

To assess if this is the case for you, you can setup your camera, then get a reference point on the live view, and then wait 30 second and see if the point has drifted on the live view. On my setup I could see the drift.

Also, if your camera has it, you can use the Electronic Front Curtain shutter mode (I think Fuji names it E-Front or something like this). This will remove any potential vibration caused by the first curtain movement.

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The manual is clear, the ibis should be turned off when on a tripod.

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