It's just settings in the encoding system, I have no idea why it's so common. In terms of backing up, according to the CCE FAQ, progressive material flaged as interlaced should be encoded using ConvertToYUY2(interlaced=true) in avisynth (assuming you are re-encoding), but other than that may be treated as progressive.
In terms of other methods, it is possible to create truely interlaced PAL when going from 24 to 25 by repeating fields e.g.
AVISource("C\test.avi",audio=false)
ConvertToYUY2()
ChangeFPS(50, 1)
SeparateFields()
SelectEvery(4, 0, 3)
Weave()
One can also use DGPulldown to achieve this using flags, which is more space efficient and it's possible to return the video to its original form by stripping flags.
But these methods result in video that is a tad jerky.
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