Let's put it in another way using Yasuo's Ultimate.
Yasuo (when he was first released, at least) was the only champion with an activation condition on his Ultimate. Because his Q3 isn't perfectly reliable, this means, ability for ability, Yasuo is noticeably weaker on a macro scale compared to most other champions because he doesn't have free access to his Ultimate. However, it does have fantastic synergy with other champions with more reliable knock ups like Malphite, Jarvan, or Nautilus.
Now let me put it this way, are synergistic mechanics wrong design and any champion with them must be removed or reworked? Should Xayah and Rakan, Lucian and Braum, Sejuani and any melee carry all be deleted because they have synergistic abilities? They are all impossible to balance perfectly due to these mechanics in their kit; alone they are naturally weaker than normal but together their combination tends to be stronger than any other two random champions in the game.
This argument also works in another direction; counter picks. Champions like Trundle, Udyr, Rammus, whose existence is entirely to spite specific champions on the enemy team. Once again this is impossible to balance perfectly; all champions of this nature are overwhelmingly powerful when picked into Sejuani, Yi, or Yasuo respectively, but are terrible blind picks and would wildly underperform if they don't have someone to counter on the enemy team.
The idea of perfect balance is a stupid one in a game as complicated as League. Unless you specifically want to water down the game such that each and every champion has a perfect 50% win rate against each and every other champion, with no specific synergy or counter pick delta, balance is a poor measurement for what you should consider as being good or bad in the game.