I don't know where people would run three versions at the same time. The information from the GnuPG project is clear: You can run GnuPG 1.x and GnuPG 2.x at the same time, but you should not have GnuPG 2.0 and GnuPG 2.1 installed at the same time, as bad things might happen.
What 3rd party software is using the keystorage mechanisms directly? Do you mean how information is output from GnuPG?
It sounds like the situation you are describing is the keystore, which has changed formats. GnuPG 2.1, as far as I can remember, will oll use the older versions keystore, but you are correct, once you have a 2.1 keystore it can't be used by GnuPG 2.0 and 1.x.
It's a tough call for the GnuPG developers and something distributions should help with. On one hand there is immense pressure to improve GnuPG, on the other hand, you have many actors who kick GnuPG around when it makes any deviation.
I would say defaulting to GnuPG 1.x is a bug and new releases of Linux, Homebrew, etc., should use GnuPG 2.0 at the very least, but better yet, use GnuPG 2.1 which has many of the things that people complain about fixed or in process of being fixed.