set matte, set channels, calculations,etc to treat & take in an account layer's own transforms.
Set Matte ignores if the layer had been transformed in some way when it is used as a track matte for ex, it treats its transformrs as well, but any matte options in any effect would ignore original transformations if there is any...

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John Hughes commented
Dropping this link here. This feature was requested by Sander Van Dijk nearly 4 years ago. I would vote on his original posting too so we can gain more traction. Realllyyyy hope they can add this feature someday.
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Roei Tzoref commented
it does treat the layer transformations if the layer is continously rasterized or collapsed. see if this helps: https://vimeo.com/274047695