For myself, the passive bonuses are generally the lowest consideration for picking a mastery, as such I like the fact that they are all set, different and provide support for a niche that aligns with the passive tree they unlock the upper half of. Balance between them is another discussion entirely as currently class, skill and passive (including skills/passives from mastery selection) balance is up for debate.
I more highly consider, ‘do I want access to the unique skill for that mastery or access to the skill behind the higher section of the passive tree for that mastery?’. If yes to either of those it’s fairly black and white that I need that mastery for my build regardless of the mastery bonuses.
Following that; ‘do I want, or in some cases need, access to some specific nodes in the upper half of any of the passive trees?’. The obvious example is Lich being so much better for supporting poison builds that I would be planning to take Lich 90% of the time for poison without ever even considering Necromancer. If I can’t substitute key passive options from one passive tree with the other for a build then I will not be considering the other mastery for it’s bonus alone. This stems from the fact the bonuses are reasonably sized and typically support the tree they are linked to, as I mentioned before.
Going deeper into that, because the mastery bonus follows the same theme as the passive tree you will find that if you read something and think ‘that mastery isn’t good for my build’ then you will also lack support from the passive tree. Outside of the common good choices for most builds of that class scattered through a lot of them anyway. In this case your issue is not the mastery bonuses not supporting your build alone but either; a different mastery supporting it better or your very specific build you’re aiming for just not having good support and thus maybe not really being viable. Not every build will be super-endgame-viable, stacked with support options to clear everything and be min-maxed across every aspect and that is fine, you can still play it. The current story map difficulty currently does not require much in the way of a build to complete.
While the option to select different passives would be welcome, more choice is always nice, you would likely find something like this: When adding in more passive options, unless they synergise with the mastery passive tree they are linked to, you just end up instead asking why we don’t have the passive tree supporting X mixture of mastery bonuses for Y build. Obviously this is not always going to be the case but it does keep coming back to the fact you can;t provide perfectly equal support for every conceivable combination of skills, skill trees and playstyle that goes into a build.
I would say that for now, holding off on adding more to the pile until we have both all our planned masteries available and a balance pass over for them we should avoid layering even more min-max options on builds. Once that is in place I personally would tweak your idea and go with packs. You get a handful of passives and pick which handful but you can’t mix and match each one. This means you can have stronger, more interesting sets of passives with less concern of people finding an odd mix that becomes the objective best for the vast majority of cases.