Your understanding of what the default is, is incorrect. “isDefault for new blocks” would be a more accurate interpretation, those existing blocks are not this variant.
Think of it this way, if I’m building a row of houses then the plans/blueprints are the default. Changing the plans does not magically transform all the houses that have already been built.
You’ve told WP when a gallery is created, these are the initial attributes to use when setting this variant. So new gallery blocks would have these attributes, assuming this variant.
Remember, variants are presets, if you create a gallery block that is not this variant, give it 6 columns, link to media, no crop, and a thumbnail, then it becomes this variant. Default values are initial values, not permanent dynamic values that change when you change the defaults.
Likewise, if you create a facebook embed, and modify its attributes to insert a twitter URL, then it becomes a twitter embed block, because they are all variants of core/embed. The attributes determine which variant a block is, not the other way around.