Also I'm wondering if there is any recommedation to improve the cloud mask detection as you can see in the image below (CLDICE mask) the default parameters for L2gen removes a lot of data.
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The cloud flagging for ocean color in l2gen is admittedly a bit conservative. The default flag is based on the reflectance (rhos) in a NIR band (865 for S3A). A threshold of 0.027 is used. you can change this by using the cloud_thresh option (pick a larger value to reduce the cloud mask).
You can also set maskcloud=0 to avoid masking data flagged as cloud. The cloud flag will still be set, but not masked at L2.