#You must make the ability check regardless
You must make the ability check regardless
Magic Item Savant states in part:
You ignore all class, race, spell, and level requirements on attuning to or using a magic item.
Spell Scrolls state in part:
If the spell is on your class's spell list but of a higher level than you can normally cast, you must make an ability check using your spellcasting ability to determine whether you cast it successfully. The DC equals 10 + the spell’s level. On a failed check, the spell disappears from the scroll with no other effect.
The ability check described above is a requirement on casting the spell successfully, but it is not a requirement on using the Spell Scroll. Making that ability check is a just part of using the Spell Scroll, and whether you succeed or fail at casting the spell, you've still used the Spell Scroll. Hence, Magic Item Savant has no interaction with this ability check.
In other words, Magic Item Savant changes whether you are capable of using a magic item, but it doesn't change how well you use it: you can use a Holy Avenger and fail to hit, likewise you can use a Spell Scroll and fail to cast its spell.