Hi Jaap,
at this level of detail, the only generic answer I can give is, ‘it’s in the open source code’. More specifically, for the Sentinelhub case, for instance:
Of course, I don’t expect most users to actually do that, so we’ll have to answer all your questions separately.
In a case like clamping of negative reflectance values, we would have to run a test ourselves to see what happens.
About the timestamps, could that be the same question as this one: