INST_ARCH    = \$(ARCHNAME)

That change alone seems to fix the problem for me.
Alternatively, I can leave the GNUmakefile in it's original state and pass INST_ARCH=\MSWin32-x64-multi-thread as one of the arguments passed to 'make'.
Both result in a perl whose @INC is:

 INST_TOP/site/lib/MSWin32-x64-multi-thread
 INST_TOP/site/lib
 INST_TOP/lib/MSWin32-x64-multi-thread
 INST_TOP/lib
[download]

Also existent is:

 INST_TOP/bin
 INST_TOP/bin/MSWin32-x64-multi-thread
[download]

I'm not entirely sure what an archnamed build should look like - but the build I've got feels right and looks sane.
I haven't tried specifying an INST_ARCH value that doesn't match $Config{archname}. (Not sure what to expect with that.)

I think I might even start building my perls this way.

Normally, for every version of perl that I build, I have 4 different configurations (ie 4 different archnames).
Building them with INST_ARCH into the same INST_TOP would make good sense and reduce duplication.

Thanks for chiming in jcb.
It's a pity you didn't get in there a bit earlier. (Would have saved me some time, effort and embarrassment ;-)

Cheers,
Rob