I did some checking for issues along the borders of the refined mesh areas, and there is indeed a small discontinuity/short invisible wall varying in height exactly at the border of the refined mesh areas. You can see where this is with the floating line of trees in the image below. In this case, the highest point I could find in the invisible boundary was ~650ft above ground level. On either side of this boundary line, it is unaffected. What this means is if you're flying very low to the ground and cross this line, you might suddenly crash.
So, if you do decide to try this, be aware that you may create short, invisible collision walls at the boundaries of your refined region.
Fortunately, each section of the USGS data covers a very large area, and it doesn't take long to convert, so it's not difficult to just convert a large enough area so that any issues like this only appear out the in the middle of nowhere or away from airports.
Disclaimer, please read:
I'm assuming that anyone here who wants to do this already knows they are tinkering with the nuts and bolts of the sim, so please, just be smart about it, and if you encounter issues due to this, don't go complaining to the IPACS team. They are already pretty reluctant about letting me share this, and not only do I not want a headache for them, but I also don't want to be the guilty party if they take issue with me telling people how to do this in the future. It's very easy to reverse this if you have issues, and I will make sure you know how to do so in the tutorial.
Ok, with that out of the way... I'll be working on the tutorial this evening and should hopefully have it posted up here in 6 hours or less!