I understand that this setting will not persist through a reboot
Uh, what? It sure does persist if you set it via esxcli properly. There used to be a bug in ESX(i) 4.0 where the setting would not persist reboots like you described, but it's been resolved since 4.0 U2:
http://www.vmware.com/support/vsphere4/doc/vsp_esxi40_u2_rel_notes.html
For devices using the roundrobin PSP the value configured for the --iops option changes after ESX host reboot
If a device that is controlled by the roundrobin PSP is configured to use the --iops option, the value set for the --iops option is not retained if the ESX host is rebooted.
This issue is resolved in this release.
Besides if it wasn't, why does your setting stay at 100 and not the default 1000?