Also after collecting the egg Sweet Scent a pokemon from the grass to the left and check its chracterictic compared to the IVs from Frame 14 or 15. That way you'll know whether you hit your Timer0 or not.
The calculate button still works but the NPCs will advance it a bit farther. When you get into the game, bring up your menu as fast as possible, then back out and accept the egg as fast as possible. By comparing the pokemon you hatch from it with the PID frames shortly after your calculated initial frame, you'll know what you need to use as a starting frame.
They aren't necessary but they give you a lot more seeds to choose from. For very specific searches (all 6 ivs, ability, encounter slot, etc) keypresses may allow you to find matches when you have none without keypresses.
NPCs don't make it that much harder. Basically, they change your starting frame. Around the daycare, they usually advance it by somewhere around four. So you usually have to try once, see where you landed and then adjust. It just adds a step. However, if I just add 4 to my starting frame and try it from there (ex. pretending your starting frame is 51 instead of 47), I often get it on my first try. Also, everstones make finding your initial frame harder because they make lots of frames look the same.
That was the only thing that made sense to me but I know you thought you checked it. Congrats on figuring it out though. I have bunches of TR Pokemon but no Venipede yet. :)