The msi package has to target either x64 or x86 and directories used in the package need to derive from a MSI defined root folder which has correct bitness. You can use Burn to chain x64 MSI package to install native files with a x86 MSI package to install the 32 bit code. (In my case the driver is signed and has two subfolders that are platform specific. To avoid breaking the driver signing all files are installed to the ProgramFiles in the x64 package, and to ProgramFiles32 tree in the x86 package.)
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