I don't pretend to know the why's or when's of the clipping limit being applied to conversions and personal documents, but...
If the document has DRM, there is no way (any more) to remove the clipping limit without first stripping the DRM.
If the document is DRM-free (as in your case), it should be possible to eliminate a clipping limit by deleting exth header type 401 with something like mobi2mobi.
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