Indeed they are. NPCs won't make it much harder as long as you stick with Frame 1. Breeding is a little different but not much. You know most everything you need to RNG anything in 5th gen except Thundurus/Tornadus now. :D
Yeah, you've got it figured out now. And you probably know but when I say a chatter I mean viewing the summary of a chatot that knows the move chatter and has a sound recorded. You don't have to back out and click summary again either. You can just use your up or down button to move away from the chatot and then go back to it. Much faster that way.
No, they both work the same way when there aren't any NPCs. Saving won't work in other places but Chatots will. However, Chatots are still much faster and since your first shot at Jolly is 48 saves away, I would either use your Chatot (has to have a custom sound learned), or get a Jolly synchronizer from me.
I think your Lax one is actually on frame 54. If you'll check the box on the left about the released roamer and then hit Calculat initial frame, it will tell you about where you'll start. Were you getting Lax with no chatters or with one?
Anything that has the wrong ivs is not from your seed and so it has nothing to do with the list, if your lax one had the right ivs and jolly is after it, one more chatot should get you flawless jolly. What frame was the lax one btw? (Since there are no NPCs, if you can copy the seed in here for me, and tell me whether you have activated/released your roamer, I can tell you exactly how many chatots you should need.)
I'd give one time/date more than two chances though you usually won't have to. If you think you calibrated with the better timer0, I'd give it at least four tries since there's always the possibility the less common timer0 will pop up on you. Still, twice on one frame and some on others with no hits isn't a good sign. You are accounting for the delay that the Parameter finder told you about, right? You usually have to hit A to start the game one second before the time your seed says.
What frame (iv) is your target on? You are definitely missing your seed for one reason or another. If you're using frame 1 (I would recommend always using frame 1 for captures) it is either a timing/keypress issue or a calibration/timer0 problem. Feel free to VM me. I'll try to help you as much as I can.