Hello JohnyJoe,
The warning messages have been introduced in the version 1.5, unless I am mistaken. But the internal behavior is the same: the camera calibration groups will be automatically split according to the EXIF information such as focal length, camera model, pixel size.
In general the use of zoom-lens is not bad, but it could be worse, if you are using "zoom" intensively moving it back and forth. EXIF data wouldn't resolve minimal difference (like 0.1mm), but for the autocalibration procedure it may be a big difference.
As for the autorotation message, it appears when the images are captured with the same camera and lens, but the some of the images are 90 degrees rotated. For example, images 4000x3000 pixels and 3000x4000 pixels will be split into different groups, as they cannot be calibrated in the same group. That's why it is recommended to disable automatic rotation of the images in the camera settings.