ArmA 2 PBO signatures are to prevent multiplayer cheating, to make sure all players are using identical addon PBO files.
To explain the compatibility: v2 signatures are extension of v1 signatures.
v2 signature can be still understood by old servers and clients, but it acts the same as v1 signature there (no new enhanced checks done). This was done to facilitate the transition. When you release an addon which targets both 1.59 and older, you can release it with a single signature.
v1 signatures can be still understood by new versions, but they do not pass when extended test is required by the server (verifiySignatures=2).
The addons should be a lot better protected now with v2 tests, the addon modification should be detected faster and more often.