Paul's suggestion is that you make a sis file that contains the registration file and the SIS1 exe that is supposed to start on boot and have it patch the installation at a later time by silently installing the sis. The question is who will launch the patching, since the exe in SIS1 has no knowledge of this patch being needed. So you would need an installer utility that does the patching
The patch_installer.exe uses the SW Installer API to perform the installation of patch.sis You will have to sign dist.sis of course.
patch.sis - !:\...\patch.sis
patch_installer.exe - !:\sys\bin\patch_installer.exe, FR, RI
With this approach you need to sign two additional SIS files: patch.sis and dist.sis
My suggestion is that you don't use an installer but a launcher:
The launcher will then be started on boot and it will start the exe that SIS1 was supposed to register. From SIS1's perspective nothing's changed.
dist_launcher.exe - !:\sys\bin\dist_launcher.exe
[dist_pUID].rsc - c:\private\...\[dist_pUID].rsc