The “Desired Retention” is a threshold evaluated card by card. If your deck is composed of 10 cards, and 5 of them have their “Estimated Retention” lower than your Threshold (let say 80%), then it will be gathered today.
But, it means that by definition, each card has an estimated retention LOWER than 80%. Worse, if you have a lot of low intervals/stability compared to your high intervals/stability, some of those cards might already have a retention way lower than 80%, it might already have dropped to 20-50%, for example.
So, it is perfectly normal that “Average Review Retention” is lower than “Expected Individual Retention”. The only way to compensate that would for Anki to give you already some reviews of some cards above your Desired Retention to compensate the very low one. But it start to defeat its purpose, and it could lead to a lot of 90% retention reviews because one already has 10% retention for that day.
It does however mean that if you want to have at least 80% retention, you should put the desired retention HIGHER than 80%. How much higher ? The more “short intervals” you have compared to the “longer intervals”, the higher !
To make it easy to understand, imagine putting FSRS desired retentino to 99%, but having a lot of cards you just learnt today. Even if FSRS would be extremely pessimistic, it will gather those cards only once per day. To get that 99%, you would probably have to have shorter intervals than 24h.
A potential improvement of Anki could be to allow such <24 reviews, now that FSRS5 (Anki 24.10RC) already compute same-day reviews for FSRS optimization. In this way, you would not have to wait for the estimated retention to drop to 20-30% before having to redo that card. You could just do it 4-5 times one day.
Of course, it’s not proven that it would help increase how fast stability will increase. But it would definitely help getting a desired retention closer than the one you get when doing reviews