@tyronius-89
Wel, I get your frustration. I too am extremely disappointed with Rare when they introduced these. I just hit level 10 Athenas 3 weeks before the patch and am extremely disappointed that they locked cosmetics behind "new" challenges that I had already completed.
With the bad excuse of: well we didn't track the exact number. While common sense dictates that to achieve the level that I had I already completed a lot of these and they didn't even bother giving us a portion, due to their choice to tag along with a legend you get Athena reputation/alliances etc. and making your level less of an indication of what you did as a legend I guess...
I for one still have not completed the Voyager etc. commendations, as I only run Athenas pretty much with others now a days, cause Rare demotivated me that much from doing them with this choice and made those commendations have little value for me based on how they were introduced. They don't reflect my achievements as a pirate legend at all and one is even unachievable in practice, 50 shrouded ones.... I have not even seen the beast once and I am a fair bit on the seas.
The numbers are the numbers and if you want them to go up, how it was implemented means you have to go out and specifically go for them. Not all these commendations are about Athena voyages and it might be nice that some can be done simultaneously, but it is what it is.
Now for Athena voyages themselves I believe they should have made it so to have 1 animal and 1 cargo run for the non devils roar versions or left them untouched. Though the no animals removed all the risk of losing the cages to be able to complete, so made that a lot less of a worry.