I had similar issues. I get the feeling that the USB3 spec doesn't have much 'play' in it's tolerances so I had constant issues with extenders.
My solution was to just connect everything to an NUC and use a micro router to connect wirelessly from my laptop. Best decision of my life. It's a little bit of messing around to get it set up, but for around $500 it's worth it. No cables to trip over in the dark, either. I know it's possibly not where you were thinking of going, but it's worth considering.
Cheers
Markus
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