Internet is full of articles about USB3 interfering WiFi on 2.4GHz. In a nutshell: problem is insufficient shielding of connectors and cables, sometimes even USB devices' printed circuit leaks RF energy into WiFi spectrum. Solution is to use different USB device which is hopefully better designed and made.

Using wifi device in the way you do (connecting to pretty distant AP which means low received signal levels) makes the effect even more prominent. You should be using a device with (highly) directional antenna for uplink, something from wireless systems product group. And kerp using your hAP ax3 as AP (and optionally router, this task can be performed by "wireless system" device as well).

Maybe there's also a todo for the Mikrotik team, this seems like a pretty standard use case for a device with only 128 MB internal storage, so maybe they could add an additional MMC card slot for storage extension if USB 3.0 is problematic, shield the port better against stuff like this or make it manually selectable wether the Port works with USB 2.0 or 3.0 drivers.

According to feedback, seen in forum, this problem doesn't seem to be particularly frequent on MT devices, so it seems that USB port engineering on MT devices is pretty good (not problematic at least). Specially so as these devices are wireless devices and I guess that engineering team is very well aware of possible problems. However, USB peripherial devices vendors might not all be ware of such things and skip a trick or two. There are some MT devices which do feature (internal) m2. slot. The problem with these connectors is that they cost some money and not all users need them (and hence want to pay the higher price). Price increase doesn't come only from costs of additional parts (ports/connectors), adding such connectivity options often means using different SoC (not all of them support all kinds of peripherial ports), probably with higher price tag as well. And we all love MT devices also for their affordable prices, don't we?

Moving your USB flash stick further away from WiFi AP sounds like a good idea, but you have to use well shielded USB extension cable to do that, otherwise results will be underwhelming.
As I already wrote, your use case seems a bit marginal to me and thus come with some quite particular problems. Which you'll have to solve yourself, not many "boxed" solutions will fit.

I actually have some little experience with tin foil (you know, I have been manufacturing tin foil hats since the '90's ).

It is not a good idea to wrap directly the USB stick in tin foil as it may overheat.

It is better if you make a small tube with cardboard that fits loosely around the stick and cover the tube with the aluminium foil, you will need at least 4 or 5 layers of the common kitchen type or 2 or 3 of the (heavier) type used by professionals.

You usually don't need to close the other end of the tube if it s long enough (let's say 10 cm at least).

Or use something like a fizzy orange tube:
https://www.rtl-sdr.com/low-cost-shield ... -rtl-sdrs/