Clear Formats does not clear formatting on characters
It appears that Clear Formats only works on whole-cell formatting. Formatting on specific characters within the text of a cell is unaffected by Clear Formats, which is probably not what anyone wants.
My suggestion is to either add another clear option where character formatting is not preserved or change Clear Formats to truly clear all formatting. Which one gets implemented depends on how important the preservation is.
Uncle Bob commented
That would be a nice option. In the meantime, here is a macro that works for me.
Dim area As range, cell As range
For Each area In Selection.Areas: For Each cell In area.Cells
cell.formula = cell.formula