I wonder why the issue [SNAP-3442] is closed now. Because the issue persists. The current implementation makes B1 unusable for some applications.
Yes, upscaling the masks might be necessary as said in the latest comment of the issue, but this is possible.
A much simpler solution would be to stay in the native resolution of B1 and ignore the up sampled 20m data. For this I have added a pull-request.
[snap-3442] masks and reflectance data at native 60m of B1 by eomasters-repos · Pull Request #86 · senbox-org/optical-toolbox
You might like to also read my discussion with the opt-mpc.
Masks not at same resolution for B1 in L2A - Data Collections / Sentinel-2 - Copernicus Data Space Ecosystem | Community forum