The "flex container intrinsic main sizes" spec-text (section 9.9.1) doesn't currently say anything special about excluding or special handling for collapsed flex items. It probably should.
I think they are intended to have zero contribution to the container's main size, based on a side-comment in the "Collapsed Items" section, section 4.4 -- that section says: "...collapsing or uncollapsing items may change the flex container’s main size", but never says precisely how. (That section does say that these items turn into zero-main-size "struts", but that happens after the container's intrinsic sizing.)
Probably https://drafts.csswg.org/css-flexbox-1/#intrinsic-main-sizes step 1 needs:
s/For each flex item/For each flex item (excluding collapsed flex items)/
...or something along those lines.
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