Particles are placed on a lattice which spacing depends on the largest particle size (this is the minimum spacing). The spacing factor can increase the spacing, setting the spacing factor to zero means there is no extra space in the lattice. The difference with Figure 4.8 is that the ratio between large and small particles is larger in your case.
If you cannot fit the initial inventory in the domain, I can think of two options (I am assuming you have a continuous particle size distribution):
Write your own particle generation code and save the data in a
particle_input.dat file to use as initial condition: 8.4. Frequently Asked Questions — MFiX 21.3 documentation
Set up a granular flow simulation with a taller domain so you can fit the desired inventory. Let is settle for a while and save the particle positions at the end of the run. Go to the Output pane and select
Save particle positions at end of run and
reset particle velocities to zero in particle_output.dat. This will save the particle data in a file called ‘particle_output.dat’. You can inspect and edit the file if necessary and if satisfactory, rename it into
particle_input.dat and use it as the initial condition for your actual simulation.