At least on part of your problem seems to be the referenced Issue.
I tried to replicate your use case. The results looked good after adding a condition. Using the flag WQSF_lsb.WATER ensures that only valid water pixels are considered.
...
</variable>
</variables>
<conditions>
<condition>
<name>condition_0</name>
<expression>WQSF_lsb.WATER</expression>
<output>true</output>
</condition>
</conditions>
<combine>OR</combine>
...
The other issue (wrong values) occurs when SNAP removes the log10 scaling from the values. In the original NetCDF file the values are log10 scaled, thus the unit lg(re g.m-3). In SNAP the log10 is removed and the unit is only g.m-3.
The devs should have a look at this. @diana_harosa @TomBlock