Except that from within the chroot you can't access files that are outside the chroot (this being the raison d'etre of a chroot). So your 32-bit-program-in-chroot can't access, eg, your home directory. You can work around this by, eg, nfs mounting the relevant directories inside the chroot (or permanently locating them inside the chroot and symlinking from the outside in) but it can get to be non-trivial to maintain.
What might work better is a custom ld-linux.so which recognised 32-bit binaries and changed all their references to /lib, /usr/lib, etc to be references to /lib32, /usr/lib32, etc (in some cases just setting the library path for them may be sufficient).
Then all that would be needed is a dpkg modification (or a wrapper) that could intercept i386 library packages (ie 32-bit ones) as they were installed and put them into /lib32, /usr/lib32, etc. Plus perhaps some apt magic to allow installing both amd64 and i386 architecture packages on the same system.
FWIW, given Debian's release schedule -- roughly every 2 years or so now -- I suspect the problem will go away by itself before there's another (sarge+1) Debian release. So probably all that is needed is a simple-as-possible work around for use in Sarge.
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