I think I see the confusion. These sorts of complex discussions are much easier in person...
Actually, the USB A ports on the Mac Mini (both M1 and Intel) are gen 1. Here's a screenshot from Apple's product page:
View attachment 2046001
And when you wrote this,
I thought you meant the gen 1/gen2 USB-A
ports on M1 Macs were reduced in speed relative to the specs, but the TB4 ports weren't. [But in fact, you weren't referring to the configuration of the ports, you were referring to the configuration of the attached drives.]
[Also, it turns out no Macs, including the Studio, offer USB-A with gen 2.]
Thus, when I suggested a workaround of using a TB4 dock (I added the suggestion of the dock, under the assumption that the OP might have his TB4 ports filled driving monitors), I meant a workaround to avoid the reduced-speed USB-A gen 1 ports. But when you said you found no gain from the TB4 dock, I now understand you didn't mean no gain vs. a direct USB-A connection, you meant no gain vs. a direct TB4. Whew!