You can tell your friends they are wrong :-) It's a biological impossibility for the long, wispy shoots you see at the branch extremities to be rootstock. And what you are seeing is entirely normal. Vigorous, immature growth is very common on many Acer species - JM's in particular - and will typically present with very long internodes and often, juvenile foliage. The result is the long wispy shoots you see and the difference in foliage appearance. It tends to be very seasonal and by this time next year, you won't notice it at all......except for possibly a similar phenomenon occurring then :-)

Since it IS seasonal and the foliage on these shoots next season should be the same as the rest of the tree, you don't NEED to do anything. If they bug you tremendously, you can simply head them back to a length comparable with the rest of the canopy. This tends to be more of a growth phenomenon associated with younger, immature trees and only with certain cultivars. They eventually outgrow it.

Thanks gardengal. Now I'm bummed I let him take some nice shoots off of two of my more recent plantings (2x peaches and creams).

Is it normal for the leaves to look totally different though? On one of my coral barks, the "new" leaves are probably 3-4x the size, although the shape is similar.

Yes, it's quite normal :-) Many Japanese maples, especially those with variegated, reticulated or unusual leaf forms, produce two kinds of foliage, adult and juvenile. Adult foliage is present on 2 year old wood and is what you'd expect for that specific cultivar. Juvenile foliage only appears on the newest growth and can be very different - lacking variegation, larger or more/less lobes, larger size or different color.