I can confirm this now that I produced two MSIs that don't have any
component rules problems. Some history of this problem can be found in
posts titled 'Does Pyro (or Torch) ignore 4-th version number?'.

I have 2 MSIs and 2 corresponding binary wixout files. Using new
patching with wixout input produced a msp file which applied
transformation to the original database (i.e. I could see that product
version was changed in ARP after patch application) but none of the
binary files were changed. In particular all updated exes and dlls had
new and larger version numbers and should have been patched too.

Using old-style patching, meaning:
-MSIs were decompressed using administrative install
-PatchCreation WiX element was used in Patch.wxs
-MsiMsp.exe was used to produce msp from pcp.

applied patch both to the database and to the installed binary files. I
could verify that all exe and dll version numbers were upped despite
*erroneous* warnings in the log produced by msimsp.exe like:

INFO Comparing Files: C:\wixpatchbin\Build2081\admin\...\some.exe
C:\wixpatchbin\Build2082\admin\.. some.exe...
INFO Comparing bytes...
  WARNING: File versions for target file:
C:\wixpatchbin\Build2081\admin\...\soome.exe and upgrade file:
C:\wixpatchbin\Build2082\admin\...\some.exe are same, while the files
itself are different.
INFO Different content...
INFO File Key: SOME.EXE is modified

These warnings come from the wrong assumption that everything related to
Windows installer should respect only 3 upper version numbers according
to an explanation given by Stefan Krueger when I asked about it on
InstallSite forum.

I can file this as a bug, unless there are suggestions on other things
to try. From my perspective Torch and Pyro are not yet in the shape to
be reliable tools for binary patching.

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