Ok, I have read the coments so here is what I can say (again, excuse my grammar)
My theory (can I call it that way?) is using a time travel system similar to the one we can see in Steins;Gate: multiple paralel timelines that exist for every possibility. Why this is important? Because that means that if one guy travel to another one timeline, the his timeline isnt affected, so he still exist and the two possible worlds ARE NOT CONNECTED AT ALL.
There are two PPGD here: The first one is the one we see in the past visions in GT, the one that has Blossom doing "something" unthinkable apparently and Him transforming into an allmighty being, this is the timeline (PPGD1 -> GT) that X comes from.
1. Powerpuff Girls Doujinshi (PpGD) and Grim Tales (GT) are NOT connected.
Despite the conclusions you can take away from reading the PpGD and GT comic by Bleedman, they are not connected together. GT is not the future and PpGD is not the past. They are two separate universes on two alternate timelines. So consider them separate universes. At some point the comics do share a origin where the timeline was one. This separation will be explained in a future story arc explaining how Samurai Jack ended up in the PpGD, and takes place in the past predating both comics. This has been confirmed by the PpGD writer, BeeAre.
We know that X has tecnology that in someway affects spacetime, why? We dont know what the bombs does, but because of Otto we know it at the very least has an spacetime effect, so we can at the very least asume that X knows his quantum phisics at a good level
3. What does the bomb in PpGD do? Is it going to go off?
We have no idea what the bomb EXACTLY does. We do know that it has something to do with time and potentially space as indicated by the comic and by BeeAre. The bomb has gone off in the comic, it is safe to assume that it will.
I believe that X is Utonium, and that is because with all his knowledge of biomechamics...................he decide to create a PPG as his most powerfull creation, one that treats him like a father and he treats her like a daughter, curiously calling her BELL (I speak spanish, and in latinoamerica, the fail sister from the cartoon series was called BELLA) WARNING! He didnt need Mojo to tell him anything about the girls to create her, thats really interesting....
X travel to the past, and because X didnt exist in the past, the result is the creation of another timeline, this is PPGD2, the one we read. Time Squad dosnt exist GT, ok, but why? We see a lot of the school kids in the past visions of GT, so why no Otto? I think I know the reason, and the reason is X itself. Otto explains that the bomb exploding is a mystery that the Time Squad hasnt resolve and, in his words, "I cant be sure, but this may be why the time squad exists!" (see The Tiger Above, The Cliff Below
chapter. In PPGD1, there was NO BOMB, so there was no REASON for the existance of the Time Squad, it fits.
But why did X travel to the past in the first place? To prevent the horrible future to exist of course!!! Of course, he has no real way to know what is going to happen, only an idea, but for him that is enough: "I'll be honest, Irken. I can't say to you what WILL happen. Only what MIGHT. While it is my tryumph, I simply cannot tell you that it is....the future" (see Two Tense
chapter; by the way, what a curious name)
So, thats it, I want to know what you think now
P.D: Dr.X and Bell appear in the Nasty Burger in GT, but that may be only a cameo XD