This is very desirable for dev or for large hex with long programming times. The thru hole has the advantage that if you stagger the holes, you can stick a pin header in there, and it stays by itself. If you were to use 0.1", you don't really gain much over using plated thru holes for your ICSP (at least for a 2 sided board). By selecting the right thickness PCB you are close enough to perfection. Use the datasheet to find the OD of the pogo pin base you are going to order, and add that to the thickness of the PCB for the spacing. You can even do DIL, if you want, using a double-sided PCB. So you can easily replace worn/broken pins. The base is sold separately it is a hollow sheath that the entire pin slides in/out, and this base is all you solder to the PCB. The shape of the soldermask can aid in keeping the pins parallel and in alignment, if you make it narrow enough. Just edit your soldermask layer so you don't get soldermask under the middle of the pin. If you use two pads per pin with large empty space in the middle, you can much more easily get the pin straight/parallel before soldering the next one in place by walking one end at a time. Make PCB, then solder the base of the pins flat against the pcb, sideways. There's no need for any fancy machining equipment. Or you just populate the male header on pcb, make up a male-female connector, clearly mark all pin 1's, glue the cable on the pickit side so it doesn't 'disappear', and be done You can also have an unpopulated/staggered 5/6pin header on the pcb, but then you are stuck using a cable with a 'live' male end and still have a 'polarity' problem. The inline header is nice because you can easily come up with a way to connect (bare wires if needed), but it is not so great when needing to connect to a number of devices frequently. Maybe I'll have to make a little adapter for my pickit3 to convert to the same thing, as I dislike the non-keyed aspect as its too easy to get wrong- its like trying to plug in a usb device into a pc- it takes about 3 attempts before its right (at least with the usb you can't screw it up, you just attempt to do so a number of time). Using an swd type connector would be the same but smaller, and maybe the prices of these things (and cables) are more normal by now (haven't checked). It also can act as a normal 5 pin header if needed with a 5pin cable or jumpers (although I have male on both ends, so is opposite of normal pickit/snap).
It is quite nice to have a keyed connector.
For my Snap adapter, I use a 10 pin keyed idc- Not exactly the greatest connector for the mcu side, as its relatively large, but they are easy to get, easy to make cables for (or get pre-made cables which are also cheap and easy to find and you may already have some).
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