I've noticed the same thing.  I fully booked her, and set all the heal masteries.  But at best I have gotten around 6.6%  on her A1 and around 12% on her A2.

For instance, when doing a Minotaur run with her as my healer and Septimus was my DPS, the most she would heal on her A1 was 2,353.  

In a Minotaur run with Lyssandra, Coldheart, Septimus, and Godseeker Aniri - - her A2 yielded heals of 20.78%.

Lyssandra  

Heals for:  9,002 HP / 43,300 MAX HP =  20.78%

Coldheart

Heals for:  5623 HP / 27,050 MAX HP =  20.78%

Septimus

Heals for:  7369 HP / 35,445 MAX HP =  20.78%

Godseeker Aniri

Heals for:  5730 HP / 27,563 MAX HP = 20.78%

I believe Max HP is the culmination of base, aritifiact, great hall, classic arena, masteries, faction guardian, and empowerment.  Like tavatka stated, are we misunderstanding what is stated in the descriptions.   Because it dosn't say  "Bonus Heal"  which would add to the amount of the initial heal and not be based on the total Max HP (but even if that were the case, the numbers still don't add up properly).  Please let me know if this is a bug or did I just waste all those books?