I got an answer from Pentair, but in case others wonder about this I am providing their answer.

They said that the pea gravel is used to aid/protect the laterals. Having it just slightly above the tops of the laterals is fine. This required 275# of 1/8-1/4" pea gravel, exactly what the spec called for.

I have added pool filter sand above, 650# of it, which provided 13.5" of freeboard from the top inside of the unit to the top of the sand surface.

In this configuration the unit is working well, with a pressure of 12 psi and flow rate of 110 gpm.

Hopefully this information will be useful to another reader of this forum.