Hmmm, I have built is successfully, with the same PACKAGECONFIG as yours, targeting rpi3-64. (Using the head of mickledore branch for oe-core, meta-oe and meta-rpi, along with "6.9" branch of meta-qt6.).
I wonder what's your provider of virtual/libgles2 and virtual/egl for this recipe? (bitbake -e qtbase | grep ^PREFERRED_PROVIDER_virtual | grep 'egl\|libgles2')
If it is mesa, are you using the standard mesa recipe from poky/oe-core, or is it from some vendor layer? Usually these dependencies supposed to provide the files qtbase is looking for.
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