At some point someone did actually get the FMV version to work on their ROM, but it required removing the existing one. I don't really know much more outside of that, there is more talk about how to make it work late in that thread. Since the FMVs still aren't finished your MSU-1 version is the better one either way, but there's a reason for an anti-patch to be present there's no reason not to include it.
If you are referring to this post:
For anyone trying to get this to work with the Bugfix and Uncensoring patch, try renaming your patched file and the msu patch to chrono_msu, instead of chrono_msu1 like it says in the included directions. I was at wits end trying to get this to work, and that solved it for me. Hopefully this will help people searching in the future.
Check out my latest post in that thread.
Also, he is 100% running the code I've adapted to your hack, the reason he needed to rename the ROM is because his PCMs are named chrono_msu-X.pcm instead of chrono_msu1-X.pcm.
If that was the only thing required to run MSU-1 on your hack (notice that my patch is newer than qwertymodo's), I wouldn't have gone through all that trouble writing and tweaking a new code for it.
As for the person who got the FMVs in, I assume he is running Darkshock's IPS patch combined with the original intro FMV IPS patch.
Darkshock's patch will have tons of problems with your hack, such as not running NMI fade-ins/outs, aswell as running into many problems that are also present in the vanilla ROM, such as getting certain areas muted after a battle.
Basically you would be trading a properly written MSU-1 soundtrack code for one full of issues with a crappy quality FMV intro.
I mean, it does make sense to include a patch to remove MSU-1, but only if the person is going to do pretty much what I did and add his own MSU-1 code aswell as add the game events through Temporal Flux to support in-game FMVs. This is a huge amount of work though; not many are capable/willing of doing such tasks.
Is this the person? https://www.youtube.com/watch?v=B_XQmpaNX4s
Video was released after MSU-1 was added to the hack.
-Chrono Trigger: Bugfix and Uncensoring Patch (Rebuilt Fd) by Chronosplit.
Mentions Darkshock's patch:
-Chrono Trigger MSU-1 hack v1.1 by Darkshock.
And you can clearly read what I've described above in one of his comments:
I have here a version without the FMV watermark and also a patch prior to the current MSU-1 that joins the video to the new soundtrack and is compatible with the various hacks and retranslations of Chrono Trigger, unfortunately it has a serious bug that disables any music after a battle and that only comes back after leaving the area, to resolve this we must wait for the original author to release its final corrected version, something that we won't have anytime soon, I'm sorry.
I am not trying to sound aggressive and/or rude, I am just curious whether that person properly patched-in the FMVs or this is just misinformation that is leading him to damaging his ROM with a not suitable MSU-1 code.
The only other proper MSU-1 patch around is qwertymodo's, and you CANNOT patch that into Bugfix and Uncensor without asm. For FMVs you also need to edit the ROM with Temporal Flux as to add specific events to trigger the FMVs, exception being the intro.