I've noticed quite a few crabapple trees in 2-5 gallon pots that look pretty
nice, but of course the lowest branches are way too high.

That is not the problem. I wouldn't trunk chop a crabapple, but you can
gradually get budding lower down on the trunk, or use a thread graft. The main
problem with nursery trees is that they are grafted, & the graft union will be
very conspicuous. Since root hardiness is not an issue with bonsai, it is
better to buy cutting grown trees which are produced for bonsai, or if you see
something in the nursery which is particularly attractive, air-layer it. Before
you buy a crabapple, read Father Fiala's book to find out which ones are
disease resistant. Don't waste time or money on those that aren't.
Iris,
Central NY, Zone 5a, Sunset Zone 40
"If we see light at the end of the tunnel, It's the light of the oncoming
train."
Robert Lowell (1917-1977)