Is this using the Kemper mic input? Would this still be the same with an external preamp with the output set so that the KPA is in the green?
That would not make a difference imo. The JVM perhaps is the amp with the highest amount of gain on the market today. Since it does not archieve this amount of gain with clipping diodes but with traditional preamp tube gain stages its unavoidable that this comes along with some noise. Similar to a 5150 indeed. Because of the noise in the red modes the KPA will have difficulties separating noise from signal in lower dynamic ranges. In fact i find it remarkable that the KPA does detect this on its own.
The solution with the JVM is using the orange modes, which use a gain stage less. Makes the tone less compressed too. Still has more gain than any other Marshall before.
Using external preamps is a thing i would not necessarily assume to archive better profiling results. Especially those expensive tube mic preamps do a lot of coloration and even compression on their own, which is nice for preprocessing vocals. With the KPA, this will most likely reduce the dynamics of your profiles. For some moody blues tones this might be nice but in general i would go for a preamp and A/D converter that is dead neutral with maximum signal/noise ratio. The KPA built in Preamps and converters are neutral, but high quality. Check my threat where i compared the DI signals.
When using a submixer if you want to use two mics or a condenser it all depends on your mixer of course. The mackie VLZ1202 that i am using is ok, but i guess the KPA mic preamp would give even better results.