Just tried the Armada companion app out and the builder works really well, but I do not know if I will be using the play tracker for activations though.
As far as the rules go, I also like the inclusion of all of the scenario diagrams, but did not see the magic rules included anywhere. The upgrades from that expansion are all included in the builder, and their individual rules do appear in completed lists, but not the battle deck lists or general magic phase rules.
The one big omission that I saw was that there is no Kingdoms of Men in the fleet builder. That is kind of forgivable though, as every KoM fleet really only needs the captain upgrade of Dead-eye McHardy + 192 points of anything else since he is the best in the game.
Overall, a really good implementation.