With Wix/MSI, there were certain executables that I could never get it to run as part of the install process. The XML would look the same as other execute commands that worked, but I could never figure out why they didn't run.
This can "kinda" be worked around with "heat.exe" (don't get me started on naming of tools in the toolchain), but even then you'll need to explicitly specify half a dozen command-line arguments (-ag -dr -cg -srd -scom -sreg -svb6 -sfrag) to make the thing work.
Run a script to enumerate the files and populate a wix file? Zip up the different parts and have the installation process unzip them?
WiX is a thin wrapper around MSI (which sucks beyond belief) and as such it suffers full blast from all the "design" decisions of the latter, not even trying to remedy the situation.
I really could pour out a full-blown rant on MSI in general and WiX in particular, but that would be wildly offtopic and of no interest to fellow HNers.