You can use a thunder team but unless you buy multiple tickets or get lucky, you'll be stuck using D'art with her HP weapon as your soul for a very long time. It's not essentially a bad thing but you won't have potential to be doing more damage than you could if you had just gone some other 100% eidolon who wouldn't be stuck using D'art. The thunder issue hasn't really gotten that much better than 'before', their SR and R himes are all still pretty mediocre/bad aside from maybe 2, while the SSRs hold all their essentials. The only reason they're manageable now is because D'art can essentially handle most of the debuffing on her own. This might change as we get more himes but that's their current state.

Dark has more leeway as it has a better variety of SR debuffers.

Though, you never know who you'll get after you start playing, you could even draw enough SSRs to make a better team than your team using the 100%.

For the 100% not seeming that great, it's because you're still new and hit so little the damage difference seems negligible. The difference becomes more notable when you have properly leveled weapons/eidolons and then compare that damage to other players of similar status who don't have 100%'s.