Minchat Bikkurim explains it as saying that even if the wrappings are pure of any other form of impurity, they still defile the hands owing to their status as ‘part’ of the Torah scroll.
Gra has a different version of the text, reading תפורות instead of טהורות. So it’s saying that only if the wrapping is stitched onto the scroll does it defile the hands.
Acknowledging a distinction between the following and a full body, the Mishna (Ohelos 4:2) says that one is allowed to burn a piece of a dead body, seemingly for convenience:
תֵּבַת הַמִּגְדָּל, יֶשׁ בָּהּ פּוֹתֵחַ טֶפַח וְאֵין בִּיצִיאָתָהּ פּוֹתֵחַ טֶפַח, טֻמְאָה בְתוֹכָהּ, הַבַּיִת טָמֵא. טֻמְאָה בַבַּיִת, מַה שֶּׁבְּתוֹכָהּ טָהוֹר, שֶׁדֶּרֶךְ ...