"Software mixer" volume starts at 100%

I use mocp with jackd and am wondering how to get moc to start without the volume being all the way up. Also, is there a way to pass the "l" function to mocp on startup?

Short answer: No.

Long answer: As I understand Jack (and someone with more knowledge
may wish to correct me), it acts as a switching service between
audio sources (e.g., MOC) and sinks (e.g., ALSA). Therefore it
does not make a lot of sense for an application to request the
current volume setting from Jack (as that is controlled by the
downstream sink). MOC has the output volume hardcoded to 100% in
the Jack sound driver on the assumption, I assume, that every other
source is doing the same and the actual output volume is being
controlled at the audio's final destination (which makes sense
to me). This could probably be parameterised as a configuration
option, but I'm not sure if that's not breaking Jack's model.

Regarding the layout: switching the values of Layout1 and Layout2
options in the configuration file should do it for you.