One thing to note, and this is for anyone patching or hacking CD games, is that the last track isn't just a 'stop' track for CDPLAY track mode. It's there as a redundant track. The system card has support for reading from this track instead, if there are problems from reading of the main track. Though I think this is game dependent. I never really researched it, other than to find out that it serves that purpose. Emulators will probably never read from it.
I tried the patched ISO you supplied, and it runs fine in mednafen. I can't burn it to CD to try on the real system - because I need to take apart my CD addon and fix it (CD spindle sitting too low, from when I re-assembled it). Also, this was never meant to be a public patch. It was a WIP that never got finished. The patch posted here, is different than the last build that I have (my ISO has more hack code in it). It's been so long, that I honestly don't know what's different about them. Maybe a bug fix; maybe I was trying to add new support for stuffs. Dunno.