There have been a few examples of this occurring in past EF5-rated tornadoes where a home was given an EF5 DI despite the subfloor still remaining. Most notably in Greensburg, Parkersburg, and Joplin.
Here’s a great example from Greensburg. Close-up photo of the site shows wall-studs were toe-nailed to bottom plate, notably around where the stairs lead to the basement on the foundation. Aerial shows a clean sweep of all debris with reasonable contextual evidence. Result is an EF5 rating.
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The homes south of town rated EF5 save for the exception of one all had their subfloors intact as well.
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Here’s an example from Parkersburg of pretty much the same thing. This home was also rated EF5.
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Aerial of additional homes rated EF5 with their subfloors remaining.
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Even the example of EF5 damage shown in the survey paper is of a home with the subfloor still intact.
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It is also worth noting these were all assigned their ratings by Tim Marshall.
I’m not really sure why it became a thing to not rate houses swept clean off their subfloors EF5, especially when it’s been done several times in the past. Like LaDue said, it shouldn’t take a fortress to be rated EF5 if the evidence is there for it.