I was able to revert to the original licenses that came with the 6610 and do the factory reset. Alas my speeds between the 5Gbe and 10Gbe systems are now even slower, and retransmits are still quite large.

It's entirely possible I did something wrong. I followed your guide this 2nd time other than reflashing the firmware and installing the licenses you kindly provide. I didn't see any need to reflash with the same versions of firmware as my initial flash worked - the R, S and POE firmwares are all updated to the version provided in the zip file.
The licenses mine came with are:
ICX6610-PREM-LIC
ICX6610-10G-LIC-POD (enabling all 8 front SFP+ ports)
I also had issues with the 2 SFP+ ports in that they wouldn't auto-negotiate. I had to go in and configure them as 10G full duplex before they came online - I didn't have to do this the first time I setup the switch, or I don't remember doing it. Perhaps that means the ICX-MACSEC-LIC isn't included in the ICX6610-PREM-LIC license? Even so, my understanding of MACSec is that it's only to enable point to point security at layer 2. Even if the PREM license doesn't include MACSec, I can't see why my speeds got even slower or why I had to manually set them to 10G full duplex.
In any case I'm going to try it again but I'm going to change things around a bit. On my new z690 system I'll pull the Intel x520 out and re-enable the onboard Marvell/Aquantia 10Gbe NIC. I'll use a CAT7 cable to connect the RJ45 from that system to one of my Wiitek modules and insert into one of the 10G enabled front SFP+ ports. I'll then install the Intel x520 NIC in my other system and disable the onboard 5Gbe NIC. The Intel x520 will be connected to the switch using a DAC cable. Then both systems will have 10G ports and hopefully the Wiitek module will perform better.
I did look into the Aquantia AQS-107 based modules and found some on eBay for $50 US each, but not sure if they are the ones that have the Aquantia chips or the Marvell chips with the smaller buffer. I see them at retailers for much more - $180 - $210 US a piece. It's also possible that the eBay ones are knock-offs as a few of the ads add the word 'compatible' after the AOM-AQS-107-B0C2-CX part number.
Anyhow, just taking a dinner break and then I'll go retry it again. Wish me luck!