Just in case someone stumbles across this again...
innounp.exe (v0.14) had different switches now, -x will extract all the files and the script
Repacking with a modified script worked well, but I had more changes to do than I thought I would have to (most likely because the original is packed with an older version)
Things I had to change:
I Had to add
DefaultGroupName=eXtreme Movie Manager
at the top of the script to fix the install group name.
Types also gave me some problems. They were comma separated:
Name: "main_program"; Description: "Main Program Files"; Types: custom,compact,full;
The commas have to be replaced by spaces like such:
Name: "main_program"; Description: "Main Program Files"; Types: custom compact full;
Else it won't even compile.
I also had to add a [Types] section before [Components]:
Name: "full"; Description: "Full installation"
Name: "compact"; Description: "Compact installation"
Name: "custom"; Description: "Custom installation"; Flags: iscustom
Also, some "dangerous" DLLs (like WININET.DLL, which probably shouldn't be included anyways...) had to have the allowunsafefiles flag added for the project to compile.
DLL wise, I noticed also that the installer overwrites blindly DAO360.DLL with the included version (no version checking, rather unprofesionnal of them). I changed it to onlyifdoesntexist instead. (let's hope it doesn't REALLY rely on DAO for database... scary thought!)
Finally, somehow when I use it with /SP- /VERYSILENT (no need for /LOADINF anymore) it still runs the app after installing. So I had to take out the [Run] section...
(I decided to leave the desktop icon in there and to delete it post-install)
To sum things up, I wouldn't say it was hard to fix by any means, but it sheds some light on a sub par installer. The app itself might be good but the author ought to fix the installer - the runtimes part anyways...
As a reward, I get a functionnal (and unattended) non-broken, non system files overwriting installer. I had been waiting on that for all too long. One less of my few "problem apps" to install on my to-do list
(at least, most others can be easily captured/repackaged) Inno setup is quite nice after all. I might use it more soon
 After finally including it on a unattended disc. It turns out it will prompt for some of the DLLs (mostly MDAC ones) to keep/replace still. I'll try adding onlyifdoesntexist to all the system DLLs or perhaps taking the obviously useless out (might be a better option after all...) Oh well.