Not quite. It is a difference in opinion between Inkscape and Fritzing. Inkscape starts an item at the bottom left corner (that is 0 0 in Inkscape coord space. Frizting connects to the center of the item in terms of the grid (it may use Inkscapes values for the coords of the item). That means that Fritzing calculates the grid based on the middle of the item but Inkscape adjusts the item based on the bottom left corner causing the offset you are seeing. If all the terminals are the same width and height both sides are happy, as long as the start x/y coords of a terminal of identical size are on .1 boundaries the alignment will be correct. The problem you are seeing is because the header connectors are 0.056 wide and high and the grove connector ones are 0.020 wide and high (or almost). That means if connector47 starts at the .1 in grid boundary as connector0 on the header, the center of connector47 will be offset .036in in x and y from the center of connector0 causing the misalignment you are seeing.
I’ve been fighting with Inkscape for close to 2 years now and just found it 
. I have stumbled across it before a couple of times but never figured out before now how to trigger it intentionally.
Yep, that’s it. You want all the pins that connect together internally to be bused so the Fritzing part acts like the real part.
Since you are putting the effort in to making the part, the choice is yours. It will work as is, and that is the easiest solution. I’d prefer to fix up the connectors to all be on the .1 grid so the part looks its best, but that will be a bit of work (easiest is to either change the size of the terminals in the grove connectors as there are less of them or do the calculations to move the center of the existing pins on to the .1 grid like the rest of them).
That is probably a good idea, because if we can get agreement on guidelines that would help with part consistancy. That said there aren’t at the moment that many of us even making parts.
Peter