If it doesn't hook into RO, then there's no problem? It looks like it's just a fancy countdown timer with the capability of contacting other people.
Would you consider Notepad a 3rd party program because you can type in the time that you killed an MVP? I highly doubt it.
Would you consider MSN a 3rd party program if you use it to tell all your friends that you killed SK at 2:30pm? Nooo.
Unless I'm totally misreading what the program does, it looks completely legal for RO.
I'd consider Notepad and MSN more of manual timers (in which you actually put effort into timing the MVPs and there's a VERY VERY VERY slim chance you won't get on the scene ASAP) so they are legal since you have to do work to track the MVP, and on Randomized Spawn times, you can't camp a MVP just by *MVP a monster and wait an hour to MVP it again*, now you have to check back between the times.
a MVP timer would remove the challenge out of MVPing because you'd always know how long it'd take the MVP to spawn, EVEN if it's randomized. Now if that happens, how about Creators lose Acid Demonstration and All MVPs are Ghost property please. And fix so the MVPs can teleport past Icewall and use Coma on you.

Because honestly, no one that's doing an honest days work of MVPing will be able to prevent a dumbassed Champ or Bio from going in and KSing the MVP, and get this: Nearly EVERY champ or bio can. All they'd have to do is use that program to find out if the MVPs spawned or not, and by the looks of it, it'd tell them so and then go find the MVP and kill it, possibly stealing it from people that need the experience.
tl;dr: just write down the times, it's probably easier and less hassle overall.