That's an interesting idea - but I see too many issues with it…
First - no knowledge of what you've mined…
fill slots 1-8 with samples of what you want to keep what ever lands in slot 9 will either be place behind the turtle or dropped. you could then use rednet to have the turtle send status updates to a console within 64 blocks to know what you've gathered so far
Second - inventory space - it might work with vanilla, (iron, gold, redstone, lapis, diamond), but add in another half dozen items (copper, tin, uranium, silver, nikolite, apatite), and there's no way to hold even one stack of the desired ores - and I figure you could only carry 7 stacks of items, since you need to have 2 slots (potentially different materials) to dig and back fill.
see above, and the same thing would happen to a turtle in quarry mode anyways. the solution is to tag team with multiple turtles. The first one picks up all ores that can't be placed back(coal, lapiz, redstone, diamonds, uranium, ect…) and then another turtle keeps all the place-able ores (iron, gold, copper, tin, silver, ect…). if your using rp2, ic2, and forestry all at the same time with all ores enabled(there's like 3 forms of copper right?) loss is inevitable but that would be the case with any turtle.
Third - time - this picture was taken from just above my docking station - a set of 4 filters - one pulls everything out of the turtle, one adds torches, one adds a small stack of cobblestone, and the other filters torches off the output pipe. To have a mole system return to a known location would require that it dig back through all the stuff it had dug and replaced already to get home and drop off items.
since turtles can mine/place directly above and below them selves the fastest solution would be to dig vertically till it hits the bottom hop one space horizontally and then dig back up to the surface and unload. its unlikely it will find more than one stack of any material and you can order it to abort and travel back the way it came if it does.
the other complexities i see is
1.handling gravel and sand (on the trip down it will have to drop the gravel sand it finds and it would only know to do that if it finds the block it placed above its head is following it)
2.natural cobble gens (not sure how to handle this one yet)
3.navigating bed rock(not impossible but not easy either)
4.finding a hole and falling into the void (there's plenty of position tracking programs to handle this assuming u know what layer you start on (or if the turtle can hear the console its been reporting to))
p.s. also certain ores appear at certain layers you might be able to use that fact to avoid the inventory problems but that means taking more time.