In principle, the "pastefromword" plugin regards basicStyle configuration. For example, if you configure CKEDITOR.config.coreStyles_bold to be <strong>, any clipboard content detected as bold will be transformed to a <strong> element.
However, if you define a basic style using attributes, e.g. like in the example given in the documentation of CKEDITOR.config.coreStyles_italic:
CKEDITOR.config.coreStyles_italic = { element : 'span', attributes : {'class': 'Italic'} };
then an <i> element from the clipboard is correctly transformed into <span class="Italic">, but afterwards, the class attribute is filtered out, so only a <span> without attributes remains, which seems to be removed later. Thus, underlined text from Word is pasted without this format.
The correct filter application order would be to filter the attributes of the clipboard content first, then apply the transformation into the (custom) basic style, but not filter again after that step.
To reproduce:
Result: Test from word is not pasted as plain text without any spans.