@jfg said:
other (negative) consequences
The Ungrouped layer method allows you to 'interlace' image layers during scene transitions. This can create some very interesting effects, since Projector layer settings are used.
However, this method is not default since by default it mixes scenes in an additive manner, where the newer Grouped by Scene option flattens each scene individually and mixes them with a more 'cinematic' crossfade not possible with the Ungrouped option.