You can run two parallel remote systems, the Cyber Commander and the EX-RT systems. Keep the ST-E3-RT in the hotshoe, and plug a Cyber Commander (or better yet, a CST) into the PC port of the camera. Use the CC to control power of the Einsteins and the ST-E3-RT to control the speedlites.
The Cyber Commander will act as a meter for the Einsteins, but not for the speedlites (as there is no way to trigger the speedlites in this configuration, and the CC does not have a "wait for flash" feature).
You can add CSRB+ receivers to the speedlites, and the Cyber Commander can meter, fire, and group them (but not power level control). However, I do not know if they would continue to be power level controlled by the ST-E3-RT. If not, you would need to manually adjust the power from the flash head.
PocketWizard TT system can control power of both types, but you are limited to 3 groups, and 6 stops of power range on the Einstein.
So there are options, but there will be compromises.
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