Electronic – Can you put a through-hole part behind an SMT part

The best advice I can give you is keep heavy stuff along the centreline. This also applies to xtal oscillators you may be using. You might also want to ensure that the mass of elements you use are balanced about the centreline of spin or you might get some heavy-duty vibration.

For small/low mass SMT components surface mount is fine but it might be worth considering glue to add extra bonding - not too much of course because the glue has mass.

Over about 10,000 g we tend to solid pot the electronics and we've not had a problem with jobs shipped over many years up to g forces over 20,000. Connectors (inter-board PCB stuff) can be a bit flaky so use those with turned pins and multi-leaf contacts (at least three).

There is a company in the US called Statek that make hi-G xtals - not cheap but if you want peace of mind I'd consider using them. Alternatively, look at Linear Technology's array of silicon oscillators - they not bad (and no moving parts other than the electrons) - I've been testing one across temperature recently and it stayed within 10 ppm/degC across 60degC.

I've never known the internal wires on a chip to fail. We always try to make sure the acceleration pushes the components onto the PCB but sometimes this is not feasible and then we pot stuff. I believe, at 6000g you should be OK not potting.

Also, It might be worth doing a spin-test on the finished article to check for vibration and anything going wrong. We do that with all our kit. Vibration we fix just like a tyre fitter does - small weights aren't preferred so we usually drill small amounts of metal off the outer casings.

Looking into the script I see

     printf("%s %5.2f %5.2f %3.0f %s %s\n",
     E.name, u2mm((xmin + xmax)/2), u2mm((ymin + ymax)/2),
     E.angle, E.value, E.package.name);

thus it must output center of component by X axis and center of component by Y axis. Further, if you look into description

#usage "<b>Data generation for mounting machines</b>\n"
   "<p>"
   "Generates files for smds on the top and bottom layers "
   "wich can be used with mounting machines. "
   "The x and y coordinates (units: mm) of the SMD elements are calculated "
   "as mean of maximum and mimimum value of the smds origin points. "
   "The calculated value does not necessarily fit with the origin "
   "point of the part in the layout."
   "All SMD elements populated in currently set assembly variant are considered."
   "<p>"
   "The syntax of the output data looks like this:"
   "<p>"
   "<tt>name x-coord y-coord rotation value package</tt>"
   "<p>"
   "<author>Author: support@cadsoft.de</author>"

It actually slightly confusing, but I tried this script on one of my projects, and SMD device with origin out of its physical center was output to the placement file with physical center of the component.

Conclusion: origin position of the component does not matter. You do not need to rework your device.